Chapter 2 Chemistry Answers

Introduction to Bioorganic Chemistry and Chemical Biology
Answers to Chapter 2
(in-text & asterisked problems)
Answer 2.1
sp3 ..
: OH
>
Basicity:
.. sp2
N
H
N
..
sp3
Basicity:
>
sp2.. R N
S
+
Basicity:
sp2.. ..
O
- .. sp
+ C
N
R
>
Introduction to Bioorganic Chemistry and Chemical Biology | A2084

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Answer
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CF
*
Nu:
*C O
Nu:
Cl
Nu:
D
N
Nu:
CH3
F B
CH3
pB
*NN

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Answer
2.3
nO
nN
..
O
..
..
N
nN
.. sp3
.. NH2
sp2 N
H B-H
B H
H
H
-

Van Vranken2.4
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Answer
A
..
n-BuNH2
H
n-Bu
H
+ N - O:
O
Cl
OEt
Cl
also acceptable...
..
n-BuNH2
OEt
Ph
Ph
..
+
OEt
H2O:
H
+
OEt
..
H A
OEt
HO
Cl
: OEt
A H
OEt
OEt
n-Bu +
N
B:
H H
H
n-Bu
H
O
+N
O
Cl
O
n-Bu +
N
B:
H H
HO
..
Ph
+
HO
H
Ph
-A:
OEt
Ph
-A:
H
OEt
O
+
Ph

OEt
O H
*HO
:Nu
(:B)
Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 2

Answer 2.5
OH
H-bond acceptors = boxed

H-bond donors = circled
HO
+H
NH
H
N
3N
NH3+
CH3
HO
HO
HO
O-

Note: amide bond resonance precludes the lone pair
OH
O
OH
of the amide NH from acting as a
hydrogen-bond acceptor.
Answer 2.6
O
H
N
N
H
O
H
N
N
H
O
N
H
H
N
N
H
H
N
Kevlar

Answer 2.7
A Keq = 10[pKa (PhOH) pKa (H20)]
Keq = 10[10 1.7)
k1 1011 M1 s1 (diffusion limit for H3O+ in water) = 1011.7 1012
Keq =
k1 1011 M1 s1 / 1012 = 0.1 M1 s1
B (H2N anions are unlikely intermediates in water.)

Keq = 10[pKa (H3N) pKa (H20)]
Keq = 10[38 1.7)
k1 1011 M1 s1 (diffusion limit for H3O+ in water) = 1039.7 1040
Keq =
k1 1011 M1 s1 / 1040 = 1029 M1 s1
The deprotonation of NH3 by H2O would be inconceivably slow.

Answer 2.8
A
O:
NH2
B:
+
OH
N
H
OH
H
+B
H
O
NH2
-O
NH
: A-
..
NH2
NH3+


Answer 2.9
HendersonHasselbalch:
[HA]
log
[HA]
Rearranged:
= pKa pH
[A]
= 10(pKa pH)
[A]
A 10(9.27.2) = 100; [HCN]/[CN] = 100:1

B 10(9.27.2) = 100; [NH4+]/[NH3] = 100:1
C 10(4.27.2) = 0.001; [PhCO2H]/[PhCO2] = 1:1000
Answer 2.10
HO - OH
Ca
O +O H
..
(HO) 2Ca
..
OH
:B
HO - OH
Ca
O
O
OH
..
O
OH
OH
OH
OH
OH
OHChemical Biology | A2117
Introduction to
Bioorganic Chemistry and
-Ca
Van Vranken
Weiss.| 978-0-8153-4214-4
Ca .
+
.
+ O&Ca
.O
+O
O.
O
O.
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R
OH
CaOH
O
OH
OH
OH
OH
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| 978-0-8153-4214-4
Note
that&the
actual
equilibrium will involve all possible diastereomers.
Answer 2.11
O
H3C
: NH3
H3C
N +
H2
NH
.. 2
H3C
- O:
NH2
H3C
NC:
+
OH2
H3C
:A
O-
: OH
H3C
NH2
CN
NH2+
H3C
NH2

Van
Vranken2.12
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Answer
A Use the following equation.

E
4 q1 q2
r
x
r12
y
r6
Only the Coulombic, first term is relevant for the chargecharge repulsion. Substitute the distances given as r into the Coulombic equation as follows.
9800 cal mol1
4 q1 q2
1.987 cal mol1 K1 298.15 K
3
= 2/3
4 q1 q2
2
In other words, the repulsive interaction potential decreases by about 33%.
B Here, only the third term for the attractive interaction is relevant, because the first
two terms can be approximated as zero. We can compare the attractive energies at
those two differences by taking the ratio.
y
36
y
= (2/3)6 = 0.088
26
Thus, the attractive interaction potential decreases by more than 90%.


Answer 2.13
H-bond donors = circled
H-bond acceptors = boxed

net dipole
net dipole
H2N
OH
O
net dipole
arene
interaction
arene
interaction
arene
interaction
O net dipole
Every part of these molecules is capable of engaging in dispersion interactions (not shown)
Introduction
to Bioorganic Chemistry and Chemical Biology | A2093
*Answer 2.14
:O:
H3C
:O:
.. H
O
..
H3C
:O:
+
:C O:
:O:
.. CH3
O
..
..
H .. O
.. H
O
..
H
: O:
+ H3C N C :
H
H

*Answer
2.16
nO
..
O:
nO
O:
D
O
H3C
n C-
..
-CH2
NH
.. 2
nN
or
- O:
actually, these "lone pairs" are
in orbitals with symmetry
H3C
nO
CH2

2.17
*Answer
A
N
HN
+
+ H
N
H2N
..
..
- N:
C
C
C
H
H
B N
C
- :C
C
H
H
C
- ..
N
- ..
N
N+
N+

2.18
*Answer
: O:
H A
: OC:
H
OCH3 A
Ph
C
Ph
OCH3
H2O
..
H2O
..
: OH
Ph: OH
C +
3
HOC OCH
Ph
+
OCH
H 3
HO
H
OH
Ph OH
C
HOC OCH
Ph
..
OCH
..
A HO
H
A H
O
O
O
H
O
H
+ H
+O H
OC
Ph
OCH3
C
Ph
OCH3
:B :B -
O
O
..
O
..O
-
OH
Ph OH
C
HOC OCH3
Ph
+
-A:
HOH OCH3
+
-A:
H
+ H
: AO
+O H
: AOC
OC
Ph
OH
Ph
OH
C
C
Ph
OH
Ph
OH
..
-O
..
-O
O
O

Van Vranken &toWeiss
| 978-0-8153-4214-4
Introduction
Bioorganic
Chemistry and Chemical Biology | A2098
Van
Vranken & Weiss | 978-0-8153-4214-4
O
O
..
O
..O
-
H B
H B
O
O
OH
OH

*Answer 2.20
pH
phenol
amine
R
2
HO
R'
Me
H
N
R
R'
R'
Me
+
R N H
R'
R'
Me
R N
R'
carboxylic acid
O
OH
R
R"
R
7
HO
R"
R
12
-O
R"
O
OR
O
OR

2.21
*Answer
HO
-O
HN
pKa 5
Cl
OH
H2N
+
pH 7
pKa' 10
Cl
OH
OH
pKa 5
O
N
OH
pKa' 10
OMe
N+
H
N
OH
N
pKa' 10
OH
pH 7
N
pKa 16

*Answer 2.24
HO
+H
H
N
3N
OH
O
HO
O-
N
H
HO
NH2
OH
N+
H
OO
OMe
pH 7
-O
O
HO
O
P
NH3+
CO2-

OH

*Answer 2.28
-A:
HO
HO
HO
-ribofuranose
..
HO +
+
H
-A:
-ribofuranose
HO
HO
A H
HO
OH
..
HO
OH
OH
HO
HO
OH
..
HO
HO
HO
A H
ribose
HO

*Answer 2.30
A 23 = 8 stereoisomers
B
D-ribose
OH
L-ribose
OH
OH
OH
O
OH
OH
OH
OH

*Answer 2.33
N C NH2
aminonitrile
N:
: NH3
H2N
+N
H H
:B
- N:
H2N
N
H

H NH3
NH
H2N
NH2
guanidine

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Chapter 2 Chemistry Answers

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Introduction to Bioorganic Chemistry and Chemical Biology

(in-text & asterisked problems)

Introduction to Bioorganic Chemistry and Chemical Biology | A2084

Introduction to Bioorganic Chemistry and Chemical Biology | A2085

Introduction to Bioorganic Chemistry and Chemical Biology | A2086

Introduction to Bioorganic Chemistry and Chemical Biology | A2087

Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 2

H-bond acceptors = boxed

Introduction to Bioorganic Chemistry and Chemical Biology | A2088

of the amide NH from acting as a

Introduction to Bioorganic Chemistry and Chemical Biology | A2089

Keq = 10[10 1.7)

k1 1011 M1 s1 (diffusion limit for H3O+ in water) = 1011.7 1012

k1 1011 M1 s1 / 1012 = 0.1 M1 s1

B (H2N anions are unlikely intermediates in water.)

Keq = 10[pKa (H3N) pKa (H20)]

Keq = 10[38 1.7)

k1 1011 M1 s1 (diffusion limit for H3O+ in water) = 1039.7 1040

k1 1011 M1 s1 / 1040 = 1029 M1 s1

The deprotonation of NH3 by H2O would be inconceivably slow.

Introduction to Bioorganic Chemistry and Chemical Biology | A2090

Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 2

A 10(9.27.2) = 100; [HCN]/[CN] = 100:1

Introduction to Bioorganic Chemistry and Chemical Biology | A2091

Introduction to Bioorganic Chemistry and Chemical Biology | A2092

A Use the following equation.

In other words, the repulsive interaction potential decreases by about 33%.

Thus, the attractive interaction potential decreases by more than 90%.

Introduction to Bioorganic Chemistry and Chemical Biology | A2117

Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 2

H-bond acceptors = boxed

Introduction to Bioorganic Chemistry and Chemical Biology | A2094

Introduction to Bioorganic Chemistry and Chemical Biology | A2096

Introduction to Bioorganic Chemistry and Chemical Biology | A2097

Introduction to Bioorganic Chemistry and Chemical Biology | A2098

Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 2

Introduction to Bioorganic Chemistry and Chemical Biology | A2100

Introduction to Bioorganic Chemistry and Chemical Biology | A2101

Introduction to Bioorganic Chemistry and Chemical Biology | A2102

Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 2

Introduction to Bioorganic Chemistry and Chemical Biology | A2106

Introduction to Bioorganic Chemistry and Chemical Biology | A2108

Introduction to Bioorganic Chemistry and Chemical Biology | A2111

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