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vi Contents
8 Alkyl Halides
6 Understanding Organic and Elimination
Reactions 219 Reactions 305
6.1 Writing Equations for Organic 8.1 General Features of
Reactions 220 Elimination 306
6.2 Kinds of Organic Reactions 221 8.2 Alkenes—The Products of Elimination
6.3 Bond Breaking and Bond Making 223 Reactions 307
6.4 Bond Dissociation Energy 227 8.3 The Mechanisms of Elimination 311
6.5 Thermodynamics 230 8.4 The E2 Mechanism 311
6.6 Enthalpy and Entropy 235 8.5 The Zaitsev Rule 316
6.7 Energy Diagrams 236 8.6 The E1 Mechanism 318
6.8 Energy Diagram for a Two-Step Reaction 8.7 SN1 and E1 Reactions 321
Mechanism 239 8.8 Stereochemistry of the E2 Reaction 322
6.9 Kinetics 241 8.9 When Is the Mechanism E1 or E2? 325
6.10 Catalysts 244 8.10 E2 Reactions and Alkyne Synthesis 326
6.11 Enzymes 245 8.11 When Is the Reaction SN1, SN2, E1, or E2? 327
Key Concepts 247 Key Concepts 331
Problems 248 Problems 333
Since the publication of Organic Chemistry in 2005, chemistry has witnessed a rapid growth in its
understanding of the biological world. The molecular basis of many complex biological processes
is now known with certainty, and can be explained by applying the basic principles of organic
chemistry. Because of the close relationship between chemistry and many biological phenomena,
Organic Chemistry with Biological Topics presents an approach to traditional organic chemistry
that incorporates the discussion of biological applications that are understood using the funda-
mentals of organic chemistry.
The organization of Organic Chemistry with Biological Topics provides the student with a logi-
cal and accessible approach to an intense and fascinating subject. The text begins with a healthy
dose of review material in Chapters 1 and 2 to ensure that students have a firm grasp of the
fundamentals. Stereochemistry, the three-dimensional structure of molecules, is introduced early
(Chapter 5) and reinforced often. Certain reaction types with unique characteristics and terminol-
ogy are grouped together. These include acid–base reactions (Chapter 2), oxidation and reduction
(Chapters 12 and 20), radical reactions (Chapter 15), and reactions of organometallic reagents
(Chapter 20). Each chapter ends with Key Concepts, end-of-chapter summaries that succinctly
organize the main concepts and reactions.
xiii
xiv Preface
Organic Chemistry with Biological Topics is supported by a chemistry of vision cis opsin
hν N
462 Chapter 12 Oxidation and Reduction trans
electrostatic potential maps to help students grasp the If unsaturated oils 11-cis-retinal
are healthier than saturated fats, why does the food industry hydrogenate
bound to opsin
oils? There are two reasons—aesthetics and shelf life. Consumers prefer the semi-solid
three-dimensional structure of molecules (including consistency
pancakes.
of margarine to a liquid oil. Imagine pouring vegetable oil on a optic
rhodopsin piecenerve
of toast or
stereochemistry) and to better understand the distribution Furthermore, unsaturated oils are more susceptible than saturated fats to oxidation at the
retina
allylic carbon atoms—the carbons adjacent to the double bond carbons—a process discussed
of electronic charge. Peanut butter is a common
in Chapter 15. Oxidation makes the oil rancid and inedible. Hydrogenating the double bonds
reduces the number of allylic carbons (also illustrated in Figure 12.4), thus reducing the like-
consumer product that disc
lihood of oxidation and increasing
membrane the shelf life of the pupil
food product. This process reflects a
contains partially hydrogenated delicate balance between providing consumers with healthier food products, while maximiz-
vegetable oil. rod cell in
ingrhodopsin
shelf lifeinto prevent
a rod cell spoilage. the retina cross-section of the eye
One other fact is worthy of note. Because the steps in hydrogenation are reversible and H
atoms areisadded
• Rhodopsin in a sequential
a light-sensitive rather
compound than concerted
located fashion,
in the membrane a cisrod
of the double
cells inbond can be
the retina of isom-
theerized to a trans double
eye. Rhodopsin containsbond. Afteropsin
the protein addition of one
bonded H atom (Step
to 11-cis-retinal via[3]
an in Mechanism
imine 12.1), an
linkage. When
light strikes this molecule,
intermediate can lose athe crowded atom
hydrogen 11-cisto
double bond
re-form isomerizes
a double bondto the
with11-trans
either isomer,
the cis and
or trans
a nerve impulse is transmitted to the brain by the optic nerve.
configuration.
As a result, some of the cis double bonds in vegetable oils are converted to trans double bonds
during hydrogenation, forming so-called “trans fats.” The shape of the resulting fatty acid chain
The complex process closely
is very different, of vision centers around
resembling this of
the shape imine derived fatty
a saturated fromacid
retinal (Figure
chain. 21.9). Thetrans
Consequently,
The central role of rhodopsin
11-cis double bond in rhodopsin creates crowding in the rather rigid side chain. When light strikes
in the visual process was
the rod cells of the retina, it is absorbed by the conjugated double bonds of rhodopsin, and the 11-cis
delineated by Nobel Laureate
George Wald of Harvard double bond is isomerized to the 11-trans arrangement. This isomerization is accompanied by a
University. drastic change in shape in the protein, altering the concentration of Ca2+ ions moving across the cell
Figure 12.4
membrane,
Partial and sending a nerve
hydrogenation of theimpulse
double to the brain,
bonds which is then
in a vegetable oil processed into a visual image.
9 pt helvetica roman
cleavage generally
R'
radical
(Chapter 7), partial hydrogenation of vegetable oil (Chapter 12), 10 pt helvetica roman
Cleave the bond
– in red.
shown
m/z = 71
–– = an allylic–– carbon—a C adjacent to a C C
• Decreasing the number of degrees of unsaturation increases
bold the melting point. Only –– chain of–– the triacylglycerol is drawn.
one long
and dopamine (Chapter 25). 10 pt helvetica radical cation
–
m/z = 86 some double bonds remain in the product.
• When an oil is partially hydrogenated, some double bonds react with H2, whereas
• Partial hydrogenation decreases the number of allylic sites (shown in blue), making a triacylglycerol less susceptible to oxidation,
thereby increasing its shelf life. • Loss of a CH39 group
pt timesalways forms a fragment
– ––
with––a mass 15 units less than the
molecular ion.
9 pt times bold – –– ––
As a result, the mass spectrum of hexane shows a peak at m/z = 71 due to CH3CH2CH2CH2CH2+.
10 pt times
Figure 13.5 illustrates –– rise to other fragments
how cleavage of other C – C bonds ––in hexane gives
smi21553_ch21_817-867.indd 842 that correspond to peaks in its mass spectrum. 03/10/15 1:25 PM
10 pt times bold – –– ––
Over 100 spectra created specifically for Organic Chemistry smi21553_ch12_455-494.indd 462
8 pt helvetica roman – –
–
[2]
–cation derived from hexane
radical –
[4] 10/20/15 11:49 AM
with Biological Topics are presented throughout the text. 8 pt helvetica bold – –[1]
– –
[2] –
m/z = 86
[3] [4]
The spectra are color-coded by type and generously labeled. 8.5 pt helvetica roman –
CH3CH2
m/z = –
–29
+
––
m/z = 43 m/z = 57 m/z = 71
Mass spectra are green; infrared spectra are red; and proton 8.5 pt helvetica bold – 100 –– ––
and carbon nuclear magnetic resonance spectra are blue. 9 pt helvetica roman – –
– ––
Relative abundance
Although entropy favors product formation in dehydration (one molecule of reactant forms two
molecules of products), –enthalpy does
10 pt helvetica roman –
– –
not, because
– the two σ bonds broken in the reactant are
10 pt helvetica bold – –
– –
–
4.4 Naming Alkanes 137
Figure 4.1
Examples of alkane
nomenclature
2,3-dimethylpentane 4-ethyl-5-methyloctane
Number to give the 1st methyl group Assign the lower number to the 1st substituent
the lower number. alphabetically: the e of ethyl before the m of methyl.
Sample Problems Sample Problem 4.1 Give the IUPAC name for the following compound.
tert-butyl at C5
5 3
• Alphabetize: the b of butyl
4 before the m of methyl
2
9
Answer: 5-tert-butyl-3-methylnonane
1
first substituent at C3
a. b. c. d.
8 pt helvetica bold – –– ––
Step [1] Name the R' group bonded to the oxygen atom as an alkyl group.
• The name of the alkyl group, ending in the suffix -yl, becomes the first part of the ester name.
8.5 pt helvetica roman – –– ––
O
8.5 pt helvetica bold – –
O– ––
O
O tert-butyl
9 pt helvetica roman – –
– ––
group
8 pt helvetica
8 ptroman
helvetica roman – ––– –– –– –– ethyl group
9Step
pt helvetica
[2] Name –
the acyl group (RCO – ) by changing
bold – the -ic–– acid ending of the parent carboxylic acid to the suffix -ate.
8 pt helvetica
8 ptbold
helvetica bold – ––– –– –– ––
• The
9 pt helvetica name of the acyl group–becomes –
light –– of the name.
–the second part
8 pt helvetica roman – –– ––
O
8.5 pt helvetica
8.5 ptroman
helvetica roman – ––– bold
8 pt helvetica –– –– O ––– ––
– ––
10 pt helvetica roman – – –– O
8.5 pt helvetica
8.5 pt bold
helvetica bold – helvetica–– bold
10 8.5
pt
– –– –– O –
––– –
––– –
–––
pt helvetica roman
derived from
acetic acid acetate derived from
8.5 pt helvetica bold – ––
– – ––
9 pt helvetica
9 pt roman
helvetica roman – – times
––
9 pt – –
– –– –
–
cyclohexanecarboxylic
– –
acid cyclohexanecarboxylate
Answer: ethyl acetate Answer: tert-butyl cyclohexanecarboxylate
– –––
9 pt helvetica
9 pt helvetica
bold bold
9 pt helvetica
– – roman
9 pt times bold
–– – ––
– ––
–– ––
– –
9 pt helvetica bold – –
– – –
–
9 pt helvetica
9 ptlight
helvetica light – –times
10 pt–– –– –
22.3D
– ––
– an ––Amide
Naming –
9 pt helvetica light – –– –
–
10 pt times bold All 1°–amides are –replacing the -ic acid, -oic acid, or -ylic acid ending with the suffix
– named by–
–
amide.
10 pt helvetica
10 pt helvetica
roman roman –roman
– helvetica––
10 pt – ––
– ––– –
– ––
898 Chapter 22 Carboxylic Acids and Their Derivatives—Nucleophilic Acyl Substitution O O
166 Chapter 4 Alkanes
–– –
10 pt helvetica
10 pt helvetica
bold bold 10–pt helvetica––
8 pt –helvetica – –– roman ––– – O–– ––
bold8 ptroman
–
helvetica – –
– ––NH2
NH2
Olestra is a polyester formed 8 ptfrom 8 long-chain
helvetica helvetica bold fatty acids
ptbold – and–
– sucrose, – –
– – the ––sweet-tasting
Key CONCePTS –
Applications and Summaries
NH 2 –
9 pt times –
– –
carbohydrate in table sugar. Naturally – occurring
– – triacylglycerols
– are also polyesters formed from
9 pt times 9 pt times – –– – – – derived from derived from derived from
long-chain fatty acids, but 9olestra
pt times
8.5 has
Alkanes
bold
pt helvetica so
8.5 pt manyroman
roman
helvetica ester units– –clustered
– – together
– acid
acetic – – –– in close
– –– benzoic acid
–
– proximity
2-methylcyclopentanecarboxylic acid
that
9 pt times 9bold
pt they
times are too hindered
bold – to8.5bept–––hydrolyzed.
General – –
–
Facts– AsAbout – olestra
a result,
–
Alkanes is
– not metabolized.
(4.1–4.3) –– – Instead, it
Key Concept Summaries helvetica
8.5 pt bold
helvetica bold –acetamide – –
– benzamide – 2-methylcyclopentanecarboxamide
– –
passes through the body unchanged,
10 pt times • providing no calories
Alkanes are composed to the
of–tetrahedral,– spconsumer.
3 – C atoms.
hybridized
9 pt helvetica •9 There are tworoman
pt roman
helvetica A 2°
types or 3° amide
of alkanes: –acyclichas –– twohaving
alkanes parts–– molecular
to
–– its structure:
–
formula
– annHacyl
C group that contains the carbonyl group
2n + 2, and
10 pt times 10 pt olestra’s
Thus, times many C – C10and C –––Hbold
pt times bonds –make
– – having
– it (RCO
similar–– )in
– and one–– or
solubility two2nto –– groupsoccurring
naturally
. alkyl bonded to triacyl-
the nitrogen atom.
Succinct summary tables reinforcing important principles and
cycloalkanes molecular formula CnH
9 pt helvetica
• 9Alkanes
pt helvetica
boldhave only
boldnonpolar C – C and C – –– no functional
– H bonds––and –
– group, so they undergo
glycerols, but its three-dimensional structure makes it inert to hydrolysis because of steric hindrance.
–– – –
– – few reactions.
10 pt times
10 bold
pt times bold – – – –
concepts are provided at the end of each chapter. 9 pt helvetica
9 ptlight
• Alkanes helvetica – -ane. ––
lightwith the suffix
are named –– –– –
–
palm oil. All soaps work in the same way, but have somewhat different properties depending on
the lipid source. The length of the carbon chain in the fatty acids and the number of degrees of
unsaturation affect the properties of the soap to some extent. xvii
Problem 22.23 What is the composition of the soap prepared by hydrolysis of the following triacylglycerol?
smi21553_ch04_128-173.indd 166 O 23/07/15 11:18 AM
O
O
O
O
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"Niin."
Iris lähti nauraen, mutta oli ollut poissa tuskin viittä minuuttia, kun
mies kuuli kaksi kertaa toistetun huudon. Hän eroitti oman nimensä
— ei Jenksin, vaan Robertin. Jotain hirveätä oli tapahtunut, sillä
huuto oli äärimmäisen epätoivoinen.
Hän juoksi sisään, tempasi kivääritelineeltä yhden kuudesta
kivääristä, jotka olivat aina ladatut ja syöksyi läpi metsän, jossa ei
nähnyt mitään, rannalle. Täällä näki hän Iriksen taistelevan kahden
villin näköisen dyakin kiinnipitelemänä, joista toinen puvusta
päättäen oli joku päällikkö ja toinen vastenmielisen näköinen
puolialaston villi. Heidän ympärillään tanssi seitsemän pyssyillä ja
parangeilla (suurilla malaijilaisveitsillä) asestettua miestä.
Tyttö kuunteli ihmetellen. Ajatteliko mies jättää hänet nyt, kun hän
oli painettuna tämän rintaa vasten? Mahdotonta! Ah, hän ymmärsi.
Villit olivat kai tulleet sinne veneellä. Merimies aikoi hyökätä heidän
kimppuunsa uudelleen. Hän ajatteli taistella yksin heidän kanssaan
eikä hän, Iris, saisi tietää mitään ennenkuin kaikki olisi ohi.
"Kuolleet!"
Varustautuminen.
Tyttö nieli sitä hiukan tehden vastustavan eleen ja Jenks joi loput.
Vasta alas tultuaan saattoi hän ymmärtää asian. Silloin hän näki,
että tapa, jolla vuoren molemmat kulmat ulkonivat, esti ylätasankoa
syrjästä näkymästä, ja edestäpäin kirkkaassa auringonvalossa
katsottuna näytti se vain mitättömältä syvennykseltä.
"Ei kai ennen, kun meitä uhkaa todellinen vaara?" huudahti tyttö.
Luolan salaisuus.
Robert Anstruther."
"Kolmekymmentä puntaa."
"Ja päivällispuku?"
"Oi, saanko puhua?" pyysi Iris. "En tahdo teitä suututtaa, mutta
minun täytyy puhua."
Hyökkäystä odotellessa.
"Vapun päivä!"
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