ORGANIC CHEMISTRY 307
CHAPTER 2 LECTURE NOTES
R. Boikess
A. Acids and Bases Review (HP. Chap 15), Remember the problems you
had with understanding this topic. It is one of the more difficult in Gen
Chem. Here we will make a “simplification.”
1. In 162 we did KA and KB. Here we do only KA (and pKA) for all
situations: neutral acids and the charged conjugate acids of neutral bases.
For example KA of NH4+ and amines etc
2. Review of Lewis Acids and Bases
An electron pair donor is a Lewis base. An electron pair acceptor is a
Lewis acid. Very general. Includes most Bronsted acids and bases. And in
addition nonhydroxylic bases such as NH3 (because of lone pair) and
nonprotonic acids such as BF3 (because of incomplete octet). Anions such as
X- and some cations (subject to restrictions on octet expansion) can be
Lewis acids.. So Ammonium is not a Lewis acid. It can’t accept electrons,
but CH3+ is a Lewis acid. It can accept electrons because it has an incomplete
octet.
3. Electrophiles and Nucleophiles
This classification is another way of thinking about Lewis Acids and
Bases. Very important because it allows us to easily characterize chemical
properties and behavior.
Since a Lewis Acid is an electron pair acceptor, it is a species that wants to
get electrons. It is an electron lover or in Greek an electrophile. The more
the species wants to get electrons, the stronger it is as a Lewis Acid or the
more electrophilic. Electrophilicity is a measure of how strongly the given
species wants to accept electrons.
A Lewis Base is an electron donor. It is a species that has an electron pair
that can be donated to something which can accept an electron pair. (an
electrophile) It is a “nucleus” lover or a nucleophile. The more the species
wants to donate the electron pair, that is the more it wants to find something
to accept its pair, the more nucleophilic. Nucleophilicity is a measure of
how strongly a species wants to donate electrons.
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B Kinetics and Thermodynamics. Review (HP 13.2-13.4, 13.8-13.10, 6.4,
17.1-17.7)
Both of these topics are very important in Orgo because they enable us to
understand organic reactions and to predict the behavior of organic
compounds in many situations.
In general, Thermo tells us whether or not something can happen. Kinetics
tells us how long it will take to happen if it can. Remember that time is not a
thermodynamic variable.
In particular, we will focus on and use
1.
2.
3.
4.
5.
Enthalpy(usually called “heat” because it is defined as the
heat flow that accompanies a process that takes place at
constant pressure) and we will refer to such measures of
chemical behavior as heat of reaction, heat of combustion,
heat of hydrogenation, bond energy, resonance energy, and
strain energy, all of which are enthalpies.
Entropy, which can be loosely understood as a measure of
disorganization, to help us understand and predict chemical
behavior.
Free Energy as a qualitative and quantitative measure of a
chemical system’s tendency to undergo change.
Rate laws, the relationship between rate and concentration,
because they give a great deal of information about how a
reaction takes place. Reaction mechanisms (how a reaction
takes place) will be one of the major themes in this course.
Activation energy, which comes from the relationship
between rate and temperature, similarly can give us a great
deal of information about reaction mechanism.
C. Overall Organization and Systematization
There are over 30 million organic compounds known and more are being
synthesized every day. We must have a way to systematize so that we can
learn and communicate.
a. Remember why there are so many compounds (C-C bonds and
chains). So one focus is to describe the carbon skeleton, which
consists of a “main” chain of C atoms with various additional C atoms
or groups of C atoms (smaller chains) attached at various points.
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b. Think of it as a “connect the dots puzzle” with “branches” allowed.
Let’s draw a big grid of dots and then connect. Do for 3 dots, 4 dots, 5
dots and 6 dots. Each different pattern corresponds to a different
carbon skeleton, which is the starting point for describing and naming
all organic compounds. Note it’s the pattern of attachment that counts,
how many dots a given dot is connected to, not how we draw it,
straight, zig-zag, or bent. See a how right angle bend doesn’t matter
for propane and butane etc. But look at (and we will return to) rings.
For 10 dots there are 75 ways, for 25 dots almost 36.8 million ways
(not counting rings). That’s why this is a whole-year course.
c. How do we go from a carbon skeleton to a compound? Every C must
have 4 bonds. Most carbons in most compounds get to 4 bonds by
bearing the requisite number of hydrogens. Introduce 1°, 2°, and 3°
carbons, related to the number of C’s to which a given C is attached.
Again, go from Kekule to condensed formulas and to condensed
formulas with parentheses. [CH3(CH2)4CH3 and CH3C(C2H5)2CH3]
Go from dots to skeletal structures. (omit terminal dots (carbons); bend
lines so that a vertex of an angle represents a dot. (carbon) as does the end of
a line. Show for propane, butane and isobutane Note branches off the main
chain. Constitutional isomers, discuss.
c. Most org cpds have at least one C that gets to 4 in some other way
than maximum H’s. One obvious way is with a multiple (double or
triple) bond, which uses 2 carbons. Show also that it can’t happen in
some structures (neopentane) and there can be no triple bonds in many
others. Discuss pentavalent carbon, which is impossible under
ordinary conditions.
d. Another way is to use atoms other than H. These are most commonly
(in order) O, N, X (halogen). S, and P. Generally there aren’t many of
these atoms compared to the number of C’s and H’s.
e. Any part of the molecule that is something other than a C bonded to
other C’s by single bonds and to H’s is called a functional group.
The chemical behavior and to some extent the physical behavior of
the molecule is determined primarily (but not entirely) by the
functional groups. Most chemical change takes place at the functional
groups. So we are going to focus on functional groups, their
chemistry, their interconversion, their preparation, and their properties
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in general. That is the overall organization of the material in the
course will be based primarily on functional groups.
f. But the carbon skeleton is also very important. Ex: methanol and
ethanol. Compare to each other and also to methane and ethane.
g. The idea of a homologous series is very useful. When a group of
compounds differ only in the number of –CH2- groups in the carbon
chain we have a homologous series. The physical properties of the
members of a homologous series change in a regular way with each
additional CH2.
D. Nomenclature
In order to communicate we must be able to give every organic compound
a name that will unambiguously identify the compound. One name must
equal one compound. Unfortunately the reverse is not true, except in a
naming system.
a. Systematic and Common names; discuss how we will deal with them.
b. What must a name do?
i. Indicate the number of C atoms
ii. Indicate the carbon skeleton
iii. Designate the type and location of the functional groups.
c. Start with compounds that have no functional groups other than
carbon-carbon multiple bonds. These compounds have only C and H
and are called hydrocarbons. If they also have no multiple bonds they
are called alkanes or saturated hydrocarbons. General formula
CnH2n+2. Show why. A C in the middle has two H’s (and two C’s), a C
at the end has 3 H’s (and 1 C) and there are two ends. For C’s in the
middle that are 3° or 4° it comes back somewhere else in an extra 1°.
Once we name these we can then use their names as the basis for
everything else by naming and locating functional groups on their
carbon skeleton. These names are systematic but some are based on
old common names and don’t seem very systematic. The system is
called the IUPAC [discuss] system. It has rules that enable us to name
any compound we can imagine. It must have a rule for very situation.
It is not possible for must chemists to know all the rules. But there are
reference works and even experts who can be consulted for new or
very complex situations.
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1. Start at an end and identify the longest continuous chain, called the
main chain. Referring to the grid of dots, the ends are the dots with
only one line. Remember that the longest chain depends only on
how the atoms are connected and not how we draw them. Go back
to the grid of dots and regard it as a puzzle. Start at an end and
trace the longest path to another end without lifting your pencil
from the paper or hitting the same dot twice. Make sure that there
are no other ends (at the start or finish) that might produce a longer
path.
2. Indicate the number of C atoms in the chain with a numerical
prefix. Memorize the first 12 (not the first 20 given in your book),
of these prefixes: [Flashcards]
i. common: meth, eth, prop, but
ii. Greek: pent, hex, hept, oct, dec
iii Latin: non
iv Latin + Greek undec, dodec
3. Add the suffix “ane” to designate no functional groups (alkane).
4. If there are no more C atoms (no branches) other than the ones in
the main chain, we are finished. Homologous series (CH2) of
straight chain or ( n-alkanes). For the first four systematic names =
common names.
5. If there are branches, we must name and locate them. Same idea
for other substituents as we will see. System is arbitrary, usually no
real chemical reasons for the names.
6. Name of Branch: The suffix indicates a branch. Drop “ane” add
“yl” Meaning of “yl” is one less H (so it can be attached). This
species is called a radical R (in this case an alkyl radical). More
generally, a radical can be any collection of C and H and even
other atoms. Key is point of attachment, which is shown by a line
CH3CH2- etc. Radicals derived from n-alkanes with missing H
(point of attachment at the end of the chain) take name (systematic
= common) from parent: show methyl, ethyl, propyl, butyl (but not
isopropyl or s-butyl because the attachment is not at the end of the
chain). For branched radicals naming is more complex, will come
back to it.
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7. Location of branch. Number the main chain, according to certain
rules. Put number in front of branch. Consider 2-methylpentane
and then 3-methylpentane.
2-methylpentane
3-methylpentane
Notice that the exact shape of the drawing is determined by the
Chem Draw software. (Remember: You can download this
software by following the directions on the course web page.)
Lowest number. [Note: no 1-methyl, 2-ethyl etc Why?]
Punctuation: Separate numbers from words or parentheses by
hyphens and from each other by commas. IUPAC names are
usually one word.
8. More than one branch. Multiplying prefixes for same branches, di,
tri, tetra, penta, Show 2,4-dimethylhexane.
Every branch has its own number. Different branches are listed
alphabetically. For this purpose multiplying prefixes and sec and
tert don’t count. But iso, neo, and cyclo are alphabetized.
9. Numbering is done from the end that gives the lowest number to
the first substituent or first different numbered substituent.
So 3,4, 6 is better than 3,5,6 and 2,7,8 is better than 3,4, 9 (decane).
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2,7,8-trimethyldecane
Note it’s not the sum. . Simply restated: Start numbering from the end
of the chain closest to a substituent.
If there is a tie then the lower number goes to the lower substituent
alphabetically: 3-ethyl-5-methylheptane. (not 5-ethyl-3-methyl)
3-ethyl-5-methylheptane
10. Branched alkanes; overlap of common and systematic for the
alkanes themselves and as parents of branched radicals.
Illustrate the branched alkanes with common names. Remember
common works only for simple cases and gives the entire
compound a name, rather than naming the pieces.
Show isobutane = 2-methylpropane, isopentane = 2-methylbutane,
isohexane = 2-methylpentane. Get the idea, meaning of iso, not
much advantage to the common name in this case.
Show neopentane= 2,2-dimethylpropane, neohexane = 2,2dimethylbutane etc. Slightly more useful than iso.
Reminder:
This type of IUPAC name is one word. Numbers in the word are
separated from each other by commas and from letters by hyphens.
11. Branched radicals. Here common names are more useful and more
used. Again simple cases: Show, isobutyl, isopentyl, isohexyl etc
and what iso means here. Compare to n-alkyl and note 1° C as the
point of attachment.
Then a few uniquely named radicals: isopropyl (contrast with
isobutyl), sec-butyl (s-butyl), and tert-butyl (t-butyl), can be
extended but usually isn’t and neopentyl, which also isn’t generally
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extended. See Table 2.6 of text. All the common names in Table
2.6 are acceptable in this course and can be used, if you wish,
in IUPAC names. So given any of these names you must be able
to write the structure.
Most chemists and other scientists use those common names and
many others that we will encounter in ordinary communication.
12. Discuss again meaning of sec and tert and lead into 1°, 2°, and
3° for radicals, functional group substituents, and even H. Note it is
always based on C (except for amines, where it is based on N).
13. Systematic names of branched radicals. Like naming branched
alkanes with two differences. (a). the suffix is “yl” not “ane”. (b)
the chain is numbered with a 1 at the point of attachment. [That
means that we can have 1-methyl or 1-ethyl as part of the name of
a branched radical]. Also the entire name of the branched radical is
put in parentheses to avoid confusion.
Show getting to systematic names: isobutyl = (2-methylpropyl),
isopentyl = (3-methylbutyl) etc. Isopropyl = (1-methylethyl) note the 1
here but not on alkanes. s-butyl = (1-methylpropyl), t-butyl = (1,1dimethylethyl), and neopentyl = (2,2-dimethylpropyl). You can see why
the common names are popular for these radicals, but also see that once
you learn the system that’s it. You must learn the system, but you still
need to know the common names for communication purposes.
Here is a challenging structure to name (You can use common or
systematic names for the branched radicals)
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E. Some Simple Functional Groups
Start with some organic derivatives of the binary hydrides of important
nonmetals. Systematize: replace one or more H’s with R’s. [Reminder about
R] Could also approach these as substituted alkanes
HX is a hydrogen halide (F, Cl, Br, I) and RX is an alkyl halide.
HOH is water. Replace one H to get ROH, the alcohols, replace both H’s
to get ROR’ the ethers (the R’s may or may not be the same).
NH3 is ammonia. Replace one H; RNH2 is a primary amine. Replace two
H’s; RNHR’ is a secondary amine. Replace all three H’s; RN(R’)R” is a
tertiary amine. Note R’s can be the same or different. Contrast this use of 1°,
2°, 3° with that for C which applies to halides and alcohols. Compare
isopropyl alcohol (2°) with isopropyl amine (1°) This is an important
exception to the rule that 1°, 2°, and 3° refer to R (or C).
The structures of these compounds reflect the structure of the parent
inorganic compound. There are of course chemical and physical differences
that arise from changing H to R.
There are many more functional groups in addition to these simple ones, as
we shall see..
a.
Nomenclature
Two main ways to name these: systematic (IUPAC) and common. In
simple cases they may be the same. Sometimes there is more than one
common name. Sometimes the common name is much simpler and is widely
used.
IUPAC names as a substituted alkane, designating the type and location of
the functional group(s). Common names are generally derived from the
parent inorganic hydride.
1. Halides RX.
a. If R has a simple or common name then the common name is often
used. It is the name of the radical followed by halide (F, Cl, Br, or
I) Methyl fluoride, ethyl bromide, isopropyl iodide, neopentyl
chloride etc. These names are derivatives of HX (hydrogen
chloride-methyl chloride) and are two words
b. If not, use the IUPAC system, which treats the X as if it is an alkyl
radical, the names are fluoro, chloro, bromo, iodo. (Could just as
well be methyl) and they are alphabetized and have the same
numerical preference as R. Names are one word. Consider these
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two names: 3-ethyl-4-fluorohexane and 3-chloro-4-ethylhexane.
Draw the structures and understand the numbering and order of the
substituents.
b.
Physical Properties
Review H.P. 11.1-11.3, 11.5-11.7, 12.1, 12.3-12.4
Major unifying theme: Physical properties are determined primarily by
polarity, secondarily by size and shape. A major factor can be H-bonding.
1. Alkanes are nonpolar.
a. Like dissolves like thus alkanes are not soluble in polar solvents.
b. Intermolecular forces in alkanes are all due to polarizability, but
they can be very important if the alkane gets big. In a homologous
series of alkanes the BP increases by about 29 K/CH2 and the ΔH
of vaporization increases by a bit more than 4 kJ/C. So an alkane
with more than about 80 C’s can’t be boiled. Why? [C-C bond
energy is 347 kJ/mol]
c. Shape can also influence boiling point: pentane = 36 °C,
isopentane 28 °C, and neopentane 9 °C. snakes and balls. Or
greater contact area = higher boiling point
d. melting point depends even more on shape because of packing, as
well as contact area. Good packing = higher melting point if there
are comparable intermolecular forces. Notice that odd numbered nalkanes melt slightly lower than expected. (Figure 2.5) This
observation can be explained by packing differences.
The closer molecules can approach each other in a crystal, the
better the packing, and the higher the melting point. The odd
numbered n-alkanes do not pack as well as the even numbered
ones. [This explanation is not in the book] Consider an n-alkane as
a zig-zag chain (a good approximation of its shape) and draw what
happens when two zig-zags are next to each other.
n-hexane
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or
n-pentane
or
Pentane
In the one with the odd number of carbons the methyl at each end
is facing the same way and they bump when the molecules try to
get close.
2. Most functional groups are polar so properties are determined by
competition between nonpolar alkyl part and polar O or N or X. The
larger the alkyl part the less the effect of the polar group on overall
properties. Solubility: 3 or 4 C atoms still can be soluble in water.
3. H-bonding especially important in determining physical properties of
organic substances in those instances where it is possible. (OH and
NH bonds)
How do we make the study of the physical and chemical properties of
millions of compounds manageable and comprehensible? Physical and
chemical properties depend on molecular structure, which has two
components, electronic (distribution of electron density in bonds and over
the molecule) and steric (the shape, 3-D arrangement of the atoms in space).
Both are very important.
F.
Representations of 3-D Structure (very important)
1. Can do it in 3-D with models. There are different types of models: ball
and stick, space filling, framework. Your kit is basically a ball and
stick type.
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2. Projections: a 3-D structure in 2-D, not all atoms need be shown by
symbols, just as they are not in condensed formulas. Different types
are useful for showing different things. Unlike the “bond-line
condensed formulas we have been using, projections often show the
H’s when they play a role in the 3-D structure.
a. Dotted line-wedge (already presented), easy and good for
designating where things are relative to each other. But not so good
for helping us to see the actual shape and spatial interactions.
b. Sawhorse, like a perspective drawing. Eye is above and to the right
of a 3-D framework model. We will use these projections
extensively when we look at rings.(Chapter 4) They are good for
seeing spatial interactions
c. Newman Projection; Note location of the eye and representations
of the C atoms. Note how flattening appears to change the angle.
Don’t forget to interpret the 2-D back to 3-D. Note how the
vertical on the front C is up.
G.
3-D Structure of some simple compounds. As we will see it’s usually
not as simple as it appears.
1. Methane, this one is simple. Ideal tetrahedral, bond angles, draw
dotted line wedge and sawhorse.
2. Ethane, not so simple. Do all this with models and draw sawhorse and
Newman projections [Figures 2-7, 2-8. 2-9 in your text] Look at these
very carefully for a long time.
a. First look at each C. It will be very close to ideal tetrahedral.
b. But what about the CH3 groups with respect to each other? Does it
matter? Explain why. These structures are all related to each other
by rotation around a single bond. They are defined as
conformations of the compound. A particular conformation is
called a conformer. (Book also uses the term “rotamer,” We will
not.) The least stable conformer is called the eclipsed. The
relative instability of the eclipsed is the result of repulsions
between the electrons in C-H bonds on the adjacent carbons.
Relative instabilities related to the shape of a molecule are due to
what is called strain. This particular type of strain is called
torsional strain. The destabilization (or torsional strain) is the
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result of bringing bonding electron pairs in C-H bonds too close to
eachother.
c. Energy differences between conformers Figure 2.10. Understand
why. Note and name two extremes eclipsed and staggered.
d. Free rotation around C-C single bond. Not totally free so it is T
dependent. Note barrier. If we lower the temperature enough we
can slow down the rotation greatly. The reason we can treat
conformations as a single compound is because the temperature on
the surface of the earth is what it is, high enough that most
rotations around single bonds are very rapid.. In outer space
(outside the satellite) staggered and eclipsed ethane would be
isomers.
3. n-Butane is more complicated. Focus on rotation around the 2-3 bond.
Methyl is much bigger than H. Thus there are two staggered
conformations of different energy and two eclipsed conformations of
different energy. Figures 2.12-2.13
The two staggered conformations are called gauche and anti. Energy
difference between them of 4 kJ/mol. This number is important because we
will use it to help explain relative energies of other compounds. It is called a
skew butane interaction. Both are much more stable than the eclipsed
conformations, which can be ignored. The relative instability of the gauche
is due to what is called steric strain, the result of atoms or groups of atoms
approaching each other too closely.
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