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Organic Chemistry Flashcards

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1
Q

CH4

A

Methane

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2
Q

C2H6

A

Ethane

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3
Q

C3H8

A

Propane

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4
Q

C4H10

A

Butane

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5
Q

C5H12

A

Pentane

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6
Q

C6H14

A

Hexane

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7
Q

C7H16

A

Heptane

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8
Q

C8H18

A

Octane

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9
Q

C9H20

A

Nonane

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10
Q

C10H22

A

Decane

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11
Q

Diol

A

Alcohols with 2 hydroxyl groups

Is a protecting group for aldehyde and ketone carbonyls

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12
Q

Geminal diols

A

Alcohols with 2 hydroxyl groups on the same carbon

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13
Q

Vicinal diols

A

Alcohols with 2 hydroxyl groups on adjacent carbons

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14
Q

2-propanol common name

A

Isopropyl alcohol

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15
Q

Ethanol common name

A

Ethyl alcohol

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16
Q

Aldehyde

A

Has a carbonyl group at the end of the chain that has at least one bond to hydrogen

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17
Q

Ketone

A

Has a carbonyl group in the middle of the chain that has two bonds to carbons

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18
Q

Aldehyde suffix

A

-al

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19
Q

Aldehyde substituent prefix

A

oxo-

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20
Q

Ketone suffix

A

-one

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21
Q

Ketone substituent prefix

A

oxo- OR keto-

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22
Q

Methanal common name

A

Formaldehyde

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23
Q

Ethanal common name

A

Acetaldehyde

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24
Q

Propanal common name

A

Propionaldehyde

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25
Q

Propanone common name

A

Acetone

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26
Q

What is the ester derivative of pentanoic acid?

A

Pentanoate

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27
Q

What is the amide derivative of pentanoic acid?

A

Pentanamide

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28
Q

What is the anhydride derivative of pentanoic acid?

A

Pentanoic anhydride

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29
Q

Alkanes

A

Hydrocarbons without any double or triple bonds

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30
Q

Alkanes formula

A

C (n) H (2 n + 2)

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31
Q

Alkanes suffix

A

-ane

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32
Q

Alkenes

A

Hydrocarbons with double bonds

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33
Q

Alkynes

A

Hydrocarbons with triple bonds

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34
Q

Alkene suffix

A

-ene

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35
Q

Alkyne suffix

A

-yne

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36
Q

Alcohols

A

Contain a hydroxyl (-OH) group

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37
Q

Alcohol suffix

A

-ol

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38
Q

Alcohol substituent prefix

A

Hydroxy-

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39
Q

Alcohol common nomenclature

A

Carbon chain name + alcohol

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40
Q

Ketone common nomenclature

A

Alkyl groups on either side in alphabetical order + ketone

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41
Q

What is the smallest ketone?

A

Acetone (a.k.a propanone)

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42
Q

Alpha-carbon

A

The carbon adjacent to the carbonyl carbon

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43
Q

What is the highest priority functional group?

A

Carboxylic acids

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44
Q

Carboxylic acid suffix

A

-oic acid

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45
Q

Methanoic acid common name

A

Formic acid

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46
Q

Ethanoic acid common name

A

Acetic acid

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47
Q

Propanoic acid common name

A

Propionic acid

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48
Q

Esters

A

Carboxylic acid derivatives where -OH is replaced with -OR

They are the condensation products of carboxylic acids with alcohols

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49
Q

Alkoxy group

A

-OR

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50
Q

Ester suffix

A

-oate

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51
Q

Ester substituent prefix

A

alkoxycarbonyl-

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52
Q

Ester common name

A

Alcohol name + carboxylic acid name used during synthesis

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53
Q

Carboxylic acid + alcohol =

A

Ester

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54
Q

Amides

A

Carboxylic acid derivatives where -OH is replaced with an amino group
They are the condensation products of carboxylic acids and ammonia or amines

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55
Q

Amide suffix

A

-amide

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56
Q

Amide substituent prefix

A

carbamoyl- OR amido-

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57
Q

How are substituents attached to the amide nitrogen designated?

A

N-

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58
Q

Anhydrides

A

Carboxylic acid derivates formed from two carboxylic acids by dehydration
They are the condensation dimers of carboxylic acids

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59
Q

Carboxylic acid + carboxylic acid (in dehydration process) =

A

Anhydride

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60
Q

Symmetric anhydride

A

Made of 2 of the same carboxylic acid

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61
Q

Asymmetric anhydride

A

Made of 2 different carboxylic acids

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62
Q

What is a cyclic anhydride made of?

A

Made from an intramolecular reaction of a dicarboxylic acid

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63
Q

Anhydride suffix

A

Anhydride in place of acid

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64
Q

The order of priority in functional groups

A
  1. Carboxylic acid
  2. Anhydride
  3. Ester
  4. Amide
  5. Aldehyde
  6. Ketone
  7. Alcohol
  8. Alkene or alkyne
  9. Alkane
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65
Q

Structural (constitutional) isomers

A

Have the same molecular formula, but different physical and chemical properties

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66
Q

Is melting point a physical or chemical property?

A

Physical

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67
Q

Is boiling point a physical or chemical property?

A

Physical

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68
Q

Is solubility a physical or chemical property?

A

Physical

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69
Q

Is density a physical or chemical property?

A

Physical

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70
Q

Conformational isomers

A

Stereoisomers with the same molecular connectivity at different points of rotation around a single (sigma) bond

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71
Q

Configurational isomers

A

Stereoisomers with differing molecular connectivity

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72
Q

Enantiomers

A

Non-superimposable mirror images

Differ at all chiral carbons, with no plane of symmetry

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73
Q

Do enantiomers have internal planes of symmetry?

A

No

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74
Q

Do enantiomers have the same physical properties

A

Yes, except rotation of plane-polarized light

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75
Q

Do enantiomers have the same chemical properties

A

Yes, except reactions in chiral environments

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76
Q

Diastereomers

A

Non-mirror-image optical isomers

Differ by at least one, but not all chiral carbons

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77
Q

Do diastereomers have the same physical properties?

A

No

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78
Q

Do diastereomers have the same chemical properties?

A

No

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79
Q

Enantiomer rotation in plane-polarized light

A

Each enantiomer’s rotation is the opposite of the other

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80
Q

Enantiomer reactions in chiral environments

A

React differently because the environment is seeking to react with only one of the enantiomers

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81
Q

Meso compound

A

Contains chiral centers and an internal plane of symmetry, the molecule is therefore achiral overall and will not rotate in plane-polarized light

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82
Q

Do meso compounds have an internal plane of symmetry?

A

Yes

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83
Q

Do meso compounds rotate in plane-polarized light?

A

No

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84
Q

Are meso compounds chiral?

A

No

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85
Q

E / Z isomers

A

Refer to arrangement of groups around a double bond

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86
Q

Z isomer

A

When the two highest priority groups are on the same side

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87
Q

E isomer

A

When the two highest priority groups are on opposite sides

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88
Q

Cahn-Ingold-Prelog priority rules

A
  1. Priority is assigned by atomic number
  2. The atom connected to the stereo center or double-bonded carbon with the highest atomic number gets the highest priority
  3. If there is a tie, one works outward from the stereo center or double-bonded carbon until the tie is broken
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89
Q

Is stereochemistry retained or inverted in a Fischer projection if we switched a pair of substituents?

A

Inverted

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90
Q

Is stereochemistry retained or inverted in a Fischer projection if we switched two pairs of substituents?

A

Retained

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91
Q

Is stereochemistry retained or inverted in a Fischer projection if we rotated the molecule 90 degrees?

A

Inverted

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92
Q

Is stereochemistry retained or inverted in a Fischer projection if we rotated the molecule 180 degrees?

A

Retained

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93
Q

Staggered conformations

A

Have groups 60 degrees apart

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94
Q

Anti-staggered conformations

A

The two largest groups are 180 degrees apart

Strain is minimized

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95
Q

Is strain minimized or maximized in anti-staggered conformations?

A

Minimized

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96
Q

Gauche staggered conformations

A

The two largest groups are 60 degrees apart

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97
Q

Types of staggered conformations

A

Anti and gauche

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98
Q

Eclipsed conformations

A

Groups are directly in front of each other (120 degrees apart)

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99
Q

Totally eclipsed conformations

A

The two largest groups are directly in front of each other

Strain is maximized (0 degrees apart)

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100
Q

Is strain minimized or maximized in totally eclipsed conformations?

A

Maximized

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101
Q

Where does the strain in cyclic molecules come from?

A

Angle strain, torsional strain and non-bonded strain

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102
Q

How is angle strain created?

A

By stretching or compressing angles from their normal size

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103
Q

How is torsional strain created?

A

By eclipsing conformations

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104
Q

Non-bonded strain

A

Created by interactions between substituents attached to non-adjacent carbons

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105
Q

How do cyclic molecules minimize strain?

A

By adopting non-planar shapes

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106
Q

How are substituents on a cyclohexane classified?

A

Axial and equatorial

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107
Q

Axial

A

Substituents are sticking up or down from the plane of the molecule

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108
Q

Equatorial

A

Substituents are in the plane of the molecule

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109
Q

What creates more non-bonded strain axial or equatorial?

A

Axial

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110
Q

Why do the largest substituents take the equatorial position?

A

To minimize strain

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111
Q

Types of conformational isomers

A

Staggered, anti-staggered, gauche staggered, eclipsed and totally eclipsed

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112
Q

How to switch between conformational isomers?

A

Change substituent rotation. No bond-breaking is required

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113
Q

How to switch between configurational isomers?

A

Bond-breaking is required

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114
Q

Types of configurational isomers

A

Enantiomers, meso compounds, diastereomers and cis-trans isomers

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115
Q

Optical activity

A

The ability of a molecule to rotate in plane-polarized light

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116
Q

d- OR (+)

A

Molecules rotate light to the right

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117
Q

l- OR (-)

A

Molecules rotate light to the left

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118
Q

Racemic mixture

A

Have equal concentrations of two enantiomers and are, therefore inactive in plane-polarized light

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119
Q

Cis-trans isomers

A

A subtype of diastereomers in which groups differ in position about an immovable bond

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120
Q

Chiral centers

A

Have four different groups attached to the central carbon

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121
Q

Relative configuration

A

Gives the stereochemistry of a compound in comparison to another molecule

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122
Q

Absolute configuration

A

Gives the stereochemistry of a compound without having to compare to other molecules
Uses the Cahn-Ingold-Prelog priority rules

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123
Q

(R) configuration

A

The substituents in a seterocenter rotate clockwise

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124
Q

(S) configuration

A

The substituents in a stereocenter rotate counterclockwise

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125
Q

Specific rotation [alpha]

A

= alpha observed / c l
alpha observed = angle observed
c = concentration in g/mL
l = diameter in dm

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126
Q

The maximum number of stereoisomers of a compound

A

2^n

n = number of chiral carbons

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127
Q

Quantum number n name

A

Principal quantum number

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128
Q

What does quantum number n describe?

A

Size

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129
Q

What is the organizational level of quantum number n?

A

Shell

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130
Q

What are the possible values for quantum number n?

A

1 to infinity

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131
Q

Quantum number l name

A

Azimuthal quantum number

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132
Q

What does quantum number l describe?

A

Shape

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133
Q

What is the organizational level of quantum number l?

A

Sub-shell

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134
Q

What are the possible values for quantum number l?

A

0 to n - 1

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135
Q

Quantum number ml name

A

Magnetic quantum number

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136
Q

What does quantum number ml describe?

A

Orientation

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137
Q

What is the organizational level of quantum number ml?

A

Orbital

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138
Q

What are the possible values for quantum number ml?

A

-l to +l

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139
Q

Quantum number ms name

A

Spin quantum number

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140
Q

What does quantum number ms describe?

A

Spin

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141
Q

What are the possible values for quantum number ms?

A

-1/2 or +1/2

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142
Q

Which is more stable: bonding or anti-bonding orbitals?

A

Bonding

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143
Q

Which has higher energy: bonding or anti-bonding orbitals?

A

Anti-bonding

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144
Q

Which has shorter bond length: double or single bonds?

A

Double

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145
Q

Which has higher bond energy: double or single bonds?

A

Double

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146
Q

Which has more molecular rigidity: double or single bonds?

A

Double

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147
Q

Which bond is strongest: sigma bond, pi bond, double bond or triple bond?

A

Triple bond

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148
Q

Which bond is weakest: sigma bond, pi bond, double bond or triple bond?

A

Pi bond

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149
Q

Which bond is stronger: sigma bond or double bond?

A

Double bond

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150
Q

What is the s character of sp hybridized orbitals?

A

50%

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151
Q

What is the s character of sp2 hybridized orbitals?

A

33%

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152
Q

What is the s character of sp3 hybridized orbitals?

A

25%

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153
Q

What is the p character of sp hybridized orbitals?

A

50%

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154
Q

What is the p character of sp2 hybridized orbitals?

A

67%

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155
Q

What is the p character of sp3 hybridized orbitals?

A

75%

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156
Q

Resonance structures

A

Differ in their placement of electrons in hybridized p-orbitals and require bond conjugation to delocalize electrons in a molecule

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157
Q

l = 0

A

Sub-shell s

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158
Q

l = 1

A

Sub-shell p

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159
Q

l = 2

A

Sub-shell d

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160
Q

l = 3

A

Sub-shell f

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161
Q

Shape of s orbital

A

Spherical

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162
Q

Shape of p orbital

A

Dumbbell

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163
Q

Bonding orbitals

A

Created by head-to-head or tail-to-tail overlap of atomic orbitals of the same sign and are energetically favorable

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164
Q

Anti-bonding orbitals

A

Created by head-to-head or tail-to-tail overlap of atomic orbitals that have opposite signs and are energetically unfavorable

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165
Q

Single (sigma) bonds

A

Contain 2 electrons

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166
Q

Double bonds

A

Contain one sigma bond and one pi bond

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167
Q

Pi bonds

A

Created by sharing electrons between two unhybridized p-orbitals that align side-by-side

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168
Q

Triple bonds

A

Contain one sigma bond and two pi bonds

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169
Q

Why are multiple bonds less flexible?

A

Because rotation is not possible when pi bonds are present

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170
Q

sp3 geometry

A

Tetrahedral, 109.5 degree angles, central carbon with 4 single bonds

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171
Q

sp2 geometry

A

Trigonal planar, 120 degree angles, central carbon with 2 single bonds and 1 double bond

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172
Q

sp geometry

A

Linear, 180 degree angles, central carbon with 1 single bond and 1 triple bond OR 2 double bonds

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173
Q

Conjugation

A

Occurs when single and multiple bonds alternate, creating a system of unhybridized p-orbitals down the backbone of the molecule through which pi electrons can delocalize

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174
Q

Why is resonance useful?

A

It increases the stability of a molecule

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175
Q

When will an acid-base reaction proceed?

A

When the acid and base react to form conjugate products that are weaker than the reactants

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176
Q

Amphoteric molecules

A

Species that can act as either acids or bases

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177
Q

Is water amphoteric?

A

Yes

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178
Q

Is bicarbonate amphoteric?

A

Yes

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179
Q

Is dihydrogen phosphate amphoteric?

A

Yes

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180
Q

pKa

A

= - log Ka

Ka = the equilibrium constant for the dissociation of an acid

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181
Q

What does pKa indicate?

A

The strength of an acid

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182
Q

What does a low pKa indicate?

A

Strong acid

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183
Q

Are alcohols acids or bases?

A

Acids

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184
Q

Are aldehydes acids or bases?

A

Acids

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185
Q

Are ketones acids or bases?

A

Acids

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186
Q

Are carboxylic acids acids or bases?

A

Acids

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187
Q

Are amines acids or bases?

A

Bases

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188
Q

Are amides acids or bases?

A

Bases

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189
Q

Nucleophilicity and electrophilicity

A

Based on relative rates of reactions and are therefore kinetic properties

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190
Q

Acidity and basicity

A

Measured by the position of equilibrium in a protonation or deprotonation reaction and are therefore thermodynamic properties

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191
Q

Is nucleophilicity a thermodynamic or kinetic property?

A

Kinetic

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192
Q

Is electrophilicity a thermodynamic or kinetic property?

A

Kinetic

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193
Q

Is acidity a thermodynamic or kinetic property?

A

Thermodynamic

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194
Q

Is basicity a thermodynamic or kinetic property?

A

Thermodynamic

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195
Q

What determines nucleophilicity?

A

Charge, electronegativity, steric hindrance and the solvent

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196
Q

Does a strong nucleophile have a more negative or more positive charge?

A

More negative

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197
Q

Is a strong nucleophile more electronegative or less electronegative?

A

Less electronegative

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198
Q

Is a strong nucleophile large or small?

A

Small

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199
Q

How does the solvent change a nucleophile’s reactivity?

A

Protic solvents protonate or hydrogen bond with the nucleophile, decreasing its reactivity

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200
Q

How does a substitution reaction proceed?

A

The nucleophile has to be stronger (more reactive) than the leaving group

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201
Q

Does a strong electrophile have a more negative or more positive charge?

A

More positive

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202
Q

How do better leaving groups increase electrophilicity?

A

They make the reaction more likely to proceed

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203
Q

Good leaving groups characteristics

A
  1. Can stabilize the extra electrons that result from heterolysis
  2. Are weak bases (the conjugate bases of strong acids)
  3. Resonance stabilization
  4. Have inductive effects from electron-withdrawing groups
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204
Q

Good oxidizing agents characteristics

A
  1. Have high affinities for electrons
  2. Have high oxidation states
  3. Get reduced as they accept electrons
  4. Contain a metal and a large number of oxygen
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205
Q

Good oxidizing agents

A

O2, O3, Cl2, MnO4-, CrO4-, CrO7^2-, pyridinium chlorochromate, metal + large number of oxygen atoms

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206
Q

Good reducing agents characteristics

A
  1. Have low electronegativities
  2. Have low ionization energies
  3. Contain a metal and a large number of hydrides
  4. Donate electrons while getting oxidized
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207
Q

Good reducing agents

A

Na, Mg, Al, Zn, NaH, CaH2, LiAlH4, NaBH4, metal + large number of hydrides

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208
Q

What are the two reactive centers of carbonyl-containing compounds?

A

Carbonyl carbon (electrophilic) and alpha-hydrogens (acidic)

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209
Q

Are carbonyl carbs electrophilic or nucleophilic?

A

Electrophilic

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210
Q

Are alpha-hydrogens acidic or basic?

A

Acidic

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211
Q

When do SN1 reactions occur?

A

They occur on tertiary carbons because there can be most easily stabilized

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212
Q

When do SN2 reactions occur?

A

They occur on methyl or primary carbons because these reactions are easily inhibited by steric hindrance

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213
Q

How to solve organic chemistry reactions?

A
  1. Know the nomenclature
  2. Identify the functional groups
  3. Identify the other reagents
  4. Identify the most reactive functional group(s)
  5. Identify the first step of the reaction
  6. Consider stereoselectivity
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214
Q

If there are no reaction conditions listed, what determines how the reaction will proceed?

A

The properties of the functional groups on the reactants themselves (acid-base; nucleophile-electrophile) will determine the outcome

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215
Q

Lewis acids

A

Electron acceptors
Have vacant orbitals
Positively polarized

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216
Q

Lewis bases

A

Electron donors
Have a lone pair of electrons
Anions

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217
Q

Bronsted-Lowry acids

A

Proton donors

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218
Q

Bronsted-Lowry bases

A

Proton acceptors

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219
Q

Acid dissociation constant (Ka)

A

= ([H+] [A-]) / [HA]
A measure of acidity
The equilibrium constant corresponding to the dissociation of an acid into a proton an its conjugate base

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220
Q

In which direction does pKa increase on the periodic table?

A

Bottom to top and left to right

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221
Q

Nucleophiles characteristics

A

Nucleus-loving
Contain lone pairs or pi bonds
High electron density
Carry negative charge

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222
Q

Are nucleophiles similar to acids or bases?

A

Bases

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223
Q

Are nucleophiles positively or negatively charged?

A

Negatively charge

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224
Q

Are amino groups nucleophilic or electrophilic?

A

Nucleophilic

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225
Q

Electrophiles characteristics

A

Electron-loving

Positively charged

226
Q

Are electrophiles positively or negatively charged?

A

Positive

227
Q

Are alcohols nucleophiles or electrophiles?

A

Electrophiles

228
Q

Are aldehydes nucleophiles or electrophiles?

A

Electrophiles

229
Q

Are ketones nucleophiles or electrophiles?

A

Electrophiles

230
Q

Are carboxylic acids nucleophiles or electrophiles?

A

Electrophiles

231
Q

Are carboxylic acid derivatives nucleophiles or electrophiles?

A

Electrophiles

232
Q

Why are alkanes and hydrogen ions never leaving groups?

A

Because they form reactive anions

233
Q

Unimolecular nucleophilic substitution (Sn1) reaction steps

A
  1. Leaving group leaves
  2. Carbocation forms b/c leaving group is gone
  3. Nucleophiles attacks the planner carbocation from either side
    The result is a racemic mixture of products
234
Q

Do SN1 reactions make racemic mixtures?

A

Yes

235
Q

Conditions that facilitate Sn1 reactions

A

More substituted carbons (because the alkyl groups can donate electron density and stabilize the positive charge of the carbocation)

236
Q

What does the rate of an SN1 reaction depend on?

A

The concentration of the substrate

rate = k [R - L]

237
Q

Bimolecular nucleophilic substitution (Sn2) reaction steps

A
  1. Nucleophile attacks at the same time the leaving group leaves
    Nucleophile must perform backside attack, which leads to an inversion of stereochemistry
238
Q

Do SN2 reactions invert stereochemistry?

A

Yes

239
Q

Conditions that facilitate Sn2 reactions

A

Less substituted carbons (because the alkyl groups create steric hinderance and inhibit the nucleophile from accessing the electrophilic substrate carbon)

240
Q

What does the rate of an SN2 reaction depend on?

A

The concentrations of both the substrate and the nucleophile

rate = k [Nu] [R - L]

241
Q

Oxidation state

A

The charge an atom would have if all its bonds were completely ionic

242
Q

Which are the most oxidized functional groups?

A

Carboxylic acids and their derivatives

243
Q

Which are the second most oxidized functional groups?

A

Aldehydes, ketones and imines

244
Q

Which are the least oxidized functional groups?

A

Alcohols, alkyl halides and amines

245
Q

Oxidation

A

An increase in oxidation state, assisted by oxidizing agents

246
Q

Primary alcohol + pyridinium chlorochromate (PCC)

A

= Aldehyde

247
Q

Primary alcohol + CrO3

A

= Carboxylic acid

248
Q

Primary alcohol + sodium dichromate (Na2Cr2O7)

A

= Carboxylic acid

249
Q

Primary alcohol + potassium dichromate (K2Cr2O7)

A

= Carboxylic acid

250
Q

Secondary alcohol + oxidizing agent (weak or strong)

A

= Ketone

251
Q

Aldehyde + oxidizing agent (weak or strong)

A

= Carboxylic acid

252
Q

Reduction

A

Decrease in oxidation state, assisted by reducing agents

253
Q

Aldehyde + lithium aluminum hydride (LiAlH4)

A

= Alcohol

254
Q

Ketone + lithium aluminum hydride (LiAlH4)

A

= Alcohol

255
Q

Carboxylic acid + lithium aluminum hydride (LiAlH4)

A

= Alcohol

256
Q

Amide + lithium aluminum hydride (LiAlH4)

A

= Amine

257
Q

Ester + lithium aluminum hydride (LiAlH4)

A

= 2 alcohols

258
Q

What do diols protect?

A

Carbonyl carbons in aldehydes and ketones

259
Q

How to protect alcohol groups?

A

Convert them to tert-butyl ethers

260
Q

Does a large nucleophile make a strong or weak conjugate acid?

A

Strong (the nucleophile is therefore a strong nucleophile)

261
Q

Why are aldehydes more reactive than ketones?

A

Have one alkyl group connected to the carbonyl, whereas ketones have two, creating more steric hindrance, lowering their reactivity

262
Q

Reactivity hierarchy of carboxylic acid derivatives towards nucleophilic attacks

A

Anhydrides > carboxylic acids and esters > amides

Derivatives of higher reactivity can form derivatives of lower reactivity, but not vice-versa

263
Q

Which has a lower pKa: ethanol or p-ethylphenol?

A

p-ethylphenol

264
Q

Why is p-ethylphenol a stonier acid (lower pKa) than ethanol?

A

Because its phenol group provides resonance and the phenol group is aromatic and an electron-withdrawing group

265
Q

Primary alcohol + strong oxidizing agent

A

= Carboxylic acid

266
Q

Primary alcohol + weak oxidizing agent

A

= Aldehyde

267
Q

Mesylate and tosylate

A

Convert an alcohol into a better leaving group
Useful for nucleophilic substitution reactions because it increases the stability of the product
They are alcohol protecting groups because oxidizing agents cannot react with them

268
Q

Pyridinium chlorochromate (PCC)

A

Weak oxidizing agent

269
Q

Aldehyde + 2 alcohol

A

= acetal

270
Q

Ketone + 2 alcohol

A

= ketal

271
Q

Acetals and ketals

A

Less reactive than aldehydes and ketones (especially to reducing agents), thereby protecting the functional groups from reacting

272
Q

How can an acetal or ketal be reverted back to aldehyde or ketone?

A

Using a catalytic acid

273
Q

Phenol oxidation =

A

Quinone

274
Q

Quinone oxidation + addition of hydroxyl groups =

A

Hydroxyquinone

275
Q

What chemical properties of ubiquinone (coenzyme Q) allow it to carry out its biological functions?

A

Ubiquinone has conjugated rings, which stabilize the molecule when accepting electrons
The long alkyl chain in the molecule allows for lipid solubility, which allows the molecule to function in the phospholipid bilayer

276
Q

Phenol

A

Benzene ring with hydroxyl groups

277
Q

Phenol prefixes

A

Ortho-, meta-, para-

278
Q

Ortho-

A

Phenol prefix that indicates the hydroxyl groups are on adjacent carbons

279
Q

Meta-

A

Phenol prefix that indicates the hydroxyl groups are separated by one carbon

280
Q

Para-

A

Phenol prefix that indicates the hydroxyl groups are on opposite sides of the ring

281
Q

Why do alcohols have high boiling and melting points?

A

Because they participate in hydrogen bonding

282
Q

Why do alcohols have high solubility?

A

Because they participate in hydrogen bonding

283
Q

Why are phenols more acidic than other alcohols?

A

Because the aromatic ring can delocalize the charge of the conjugate base

284
Q

Example of electron-donating group

A

Alkyl groups

285
Q

Why do alkyl groups decrease acidity?

A

They destabilize negative charges due to their electron-donating nature

286
Q

Example of electron-withdrawing group

A

Electronegative atoms and aromatic rings

287
Q

Why do electron-withdrawing groups increase acidity?

A

They stabilize negative charges

288
Q

What is mesylate’s functional group?

A

-SO3CH3

289
Q

What is mesylate derived from?

A

Methanesulfonic acid

290
Q

What is tosylate’s functional group?

A

-SO3C6H4CH3

291
Q

What is tosylate’s derived from?

A

Toluenesulfonic acid

292
Q

Deprotection reaction

A

Converting acetal or ketal back to aldehyde or ketone by a catalytic acid

293
Q

Quinone

A

Resonance-stabilized electrophile

294
Q

Examples of quinones

A

Vitamin K1 (phylloquinone) and Vitamin K2 (menaquinone)

295
Q

Vitamin K1

A

Phylloquinone

296
Q

Vitamin K2

A

Menaquinone

297
Q

Ubiquinone (coenzyme Q)

A

Acts as an electron acceptor in Complexes I, II and III of the electron transport chain

298
Q

Ubiquinol

A

The reduced version of ubiquinone (coenzyme Q)

299
Q

Why are tertiary alcohols difficult to oxidize?

A

Because there is no hydrogen attached to the carbon with the hydroxyl group

300
Q

Factors increasing the boiling point

A

Increasing size of alkyl chain because of increased van der Waals attractions
Hydrogen bonding

301
Q

What is the oxidizing agent in a Jones oxidation reaction?

A

Dilute sulfuric acid

302
Q

How to convert phenols into hydroxyquinones?

A
  1. Phenol –> quinone through oxidation

2. Quinone –> hydroxyquinone through oxidation

303
Q

How to convert acetal to a carbonyl and a dialcohol?

A

Treatment with aqueous acid

304
Q

Given an alkane, an aldehyde and alcohol with equal-length carbon chains: what is their arrangement in increasing boiling points?

A
  1. Alkane
  2. Aldehyde: has dipole
  3. Alcohol: can hydrogen bond
305
Q

Is the carbonyl carbon electrophilic or nucleophilic and why?

A

Electrophilic, because it’s partially positive since the oxygen pulls the electrons away from the oxygen

306
Q

How to form an aldehyde?

A

Primary alcohol + PCC

Carboxylic acid + reducing agent

307
Q

How to form a ketone?

A

Secondary alcohol + any oxidizing agent

308
Q

What happens when an aldehyde or ketone is reacted with one equivalent of an alcohol in acidic conditions? What kind of reaction is it?

A

Aldehyde: Hemiacetal
Ketone: Hemiketal
Nucleophilic addition

309
Q

What happens an an aldehyde or ketone is reacted with two equivalents of alcohol in acidic conditions? What kind of reaction is it?

A

Aldehyde: Acetal
Ketone: Ketal
Nucleophilic addition (first step to hemiacetal or hemiketal) then nucleophilic substitution (second step to acetal or ketal)

310
Q

What type of reaction occurs when nitrogen, or nitrogen-containing derivates react with aldehydes and ketones?

A

Nucleophilic substitution and dehydration

311
Q

What functional group forms when nitrogen, or nitrogen-containing derivates react with aldehydes and ketones?

A

Imine, oximes, hydrazones and semicarbazones

312
Q

What functional group forms when HCN reacts with an aldehyde or ketone?

A

Cyanohydrin

313
Q

Is the product of a reaction between HCN and an aldehyde or ketone stable?

A

Yes

314
Q

What functional group is formed when an aldehyde is oxidized?

A

Carboxylic acid

315
Q

What are common oxidizing agents that can oxidize an aldehyde to a carboxylic acid?

A

KMnO4, CrO3, Ag2O and H2O2

316
Q

What functional group is formed when aldehydes and ketones are reduced?

A

Aldehyde: Primary alcohol
Ketone: Secondary alcohol

317
Q

What are common reducing agents that can reduce aldehydes and ketones to alcohols?

A

NaBH4 and LiAlH4

318
Q

Are aldehydes terminal or internal functional groups?

A

Terminal

319
Q

Aldehyde suffice if they are in a ring

A

-carbaldehyde

320
Q

Are ketones terminal or internal functional groups?

A

Internal

321
Q

Why do carbonyl-containing compounds have higher boiling points than equivalent alkanes?

A

Because they have dipole interactions

322
Q

Why do alcohols have higher boiling points than compounds containing carbonyls?

A

Because they can participate in hydrogen bonding

323
Q

What happens when a nucleophile attacks and forms a bond with a carbonyl carbon?

A

Electrons in the pi bond are pushed to the oxygen atom
If there is no good leaving group (aldehydes and ketones), the carbonyl will remain open and is protonated to form an alcohol
If there is a good leaving group (carboxylic acids and derivates), the carbonyl will reform and kick off the leaving group

324
Q

Hydration reaction

A

Water adds to a carbonyl, forming a geminal diol

325
Q

What functional group results when an immune tautomerizes?

A

Enamine

326
Q

Why are hemiacetals and hemiketals difficult to isolate?

A

They keep reacting to form acetals and ketals because they are very unstable. The hydroxyl group is rapidly protonated and is lost as water under acidic conditions, leaving behind a reactive carbocation. Once the alcohol has been added, the acetal and ketal become more stable as the newly added group is more stable since it is less likely to become protonated and leave, unlike -OH.

327
Q

Can PCC completely oxidize a secondary alcohol?

A

Yes (to ketone)

328
Q

Water + Carbonyl carbon

A

= Geminal diol

329
Q

Why are the alpha-hydrogens of aldehydes and ketones acidic (i.e. they deprotonate easily)?

A

Due to the inductive and resonance effects the carbonyl group offers. The electronegative oxygen atom pulls electron density from the C-H bond, weening it. Once deprotonated, the resonance stabilization of the negative charge between the alpha-carbon, carbonyl carbon and electron-withdrawing carbonyl oxygen increases the stability of this form.

330
Q

Which alpha-hydrogens are more acidic: the ones on aldehydes or the ones on ketones?

A

Aldehydes

331
Q

Why are the alpha-hydrogens on aldehydes more acidic than the ones on ketones?

A

Due to the electron-donating characteristics of the second alkyl group in ketones, the carbanion is destabilized, which slightly disfavors the loss of the alpha-hydrogens in ketones as compared to aldehydes

332
Q

How does steric hindrance affect the relative reactivity of aldehydes and ketones?

A

Aldehydes are more reactive than ketones because they are less stericaly hindered since they have one R group and one H group, while ketones have 2 R groups. The additional alkyl group in ketones gets in the way and makes for a higher-energy, crowded intermediate.

333
Q

Tautomers

A

Isomers that can be interconverted by the movement of a hydrogen and a double bond

334
Q

Which tautomer of aldehydes and ketones is thermodynamically favored: keto or enol?

A

Keto

335
Q

Which role does the enolate carbanion play in organic reactions: nucleophile, electrophile, oxidizing agent or reducing agent?

A

Nucleophiles

336
Q

What conditions favor the kinetic enolate form?

A

Because the kinetic enolate forms rapidly and can interconvert with the thermodynamic form if given time, the kinetic form is favored by fast, irreversible reactions, such as with a strong, sterically hindered base, and lower temperatures.

337
Q

What conditions favor the thermodynamic enolate form?

A

The thermodynamic enolate is favored by slower, reversible reactions, with weaker or smaller bases, and higher temperatures.

338
Q

What species acts as the nucleophile in aldol condensation?

A

The enolate carbanion (the deprotonated aldehyde or ketone)

339
Q

What species acts as the electrophile in an aldol condensation?

A

The keto form of the aldehyde or ketone

340
Q

Retro-aldol reaction

A

The reverse of an aldol reaction: a bond between the alpha- and beta-carbons of a carbonyl is broken

341
Q

What conditions favor retro-aldol reactions?

A

The addition of base and heat

342
Q

Which reactions can aldol condensation be classified under?

A

Condensation reaction (two molecules are joined to form a single molecule with the loss of a small molecule), dehydration reaction (water is lost), nucleophile-electrophile reaction (a nucleophile pushes an electron pair to form a bond with an electrophile)

343
Q

Alpha-hydrogens

A

Hydrogens attached to the alpha-carbon

344
Q

Are alpha-hydrogens acidic or basic?

A

Acidic

345
Q

How can alpha-hydrogens be removed?

A

With a strong base

346
Q

Does the electron-withdrawing oxygen of the carbonyl strengthen or weaken the C-H bonds on the alpha-carbon?

A

Weaken

347
Q

Enolate

A

Results from the deprotonation of the alpha-carbon and is stabilized by resonance with the carbonyl

348
Q

How is the enolate form stabilized?

A

Resonance due to the carbonyl carbon

349
Q

Do aldehydes and ketones exist in the keto form or the enol form?

A

Keto

350
Q

How can the enol form become enolate?

A

It can be deprotonated

351
Q

Are enolates good nucleophiles or electrophiles?

A

Nucleophiles

352
Q

Michael addition

A

An enolate attacks and alpha,beta-unsaturated carbonyl, creating a bond

353
Q

Does an imine have a tautomer?

A

Yes, enamine

354
Q

Which tautomer is more common: imine or enamine?

A

Enamine

355
Q

Aldol condensation

A

The aldehyde or ketone acts as both nucleophile and electrophile, resulting in the formation of a carbon-carbon bond in a new molecule called an aldol

In the presence of a base, the alpha-hydrogen is abstracted from an aldehyde, forming the enolate ion (RCHO-). This enolate ion then attacks the carbonyl group of the other aldehyde molecule, forming the aldol

356
Q

Aldol

A

Contains both an aldehyde and an alcohol functional group

357
Q

Steps of an aldol condensation reaction

A
  1. Condensation
  2. Dehydration
    Result: alpha,beta-unsaturated carbonyl
358
Q

Aldehyde or ketone + lithium diisopropylamide (LDA)

A

= More nucleophilic enolate carbanion

359
Q

Lithium diisopropylamide (LDA)

A

Strong base

360
Q

How to stop an aldol condensation after the aldol formation (i.e. skipping the dehydration step)?

A

Adding a strong acid

361
Q

What is the most important step in a retro-aldol reaction?

A

Breaking the carbon-carbon bond to form two aldehydes, two ketones or one of each

362
Q

What is the most important step in an aldol condensation reaction?

A

Combining two aldehydes, two ketones or one of each

363
Q

What causes the relatively high acidity of carboxylic acids?

A

The electron-withdrawing oxygen atoms in the functional group and the high stability of the carboxylate anion, which is resonance stabilized by delocalization with two electronegative oxygen atoms

364
Q

Between a monocarboxylic acid, a dicarboxylic acid, and a dicorboxylix acid that has been deprotonated once, which will be the most acidic?

A

A dicaboxylic acid would be the most acidic, as the second carboxyl group is electron-withdrawing and, therefore, contributes to even higher stability of the anion after loss of the first hydrogen.
A monocarboxylic acid is more acidic than a deprotonated dicarboxylic acid because the carboxylate anion is electron-donating and destabilizes the product of the second deprotonation step, resulting in decreased acidity.

365
Q

What effects do additional substituents have on the acidity of carboxylic acids?

A

Electron-withdrawing substituents make the anion more stable and, therefore, increase acidity.
Electron-donating substituents destabilize the anion, causing the carboxylic acid to be less acidic.
The closer the substituent is to the carboxylic acid on the molecule, the stronger the effect will be.

366
Q

Amides are formed by reaction with:

A

Ammonia or an amine

367
Q

Esters are formed by reaction with:

A

Alcohol

368
Q

Anhydrides are formed by reaction with

A

Another carboxylic acid

369
Q

Mechanism of nucleophilic acyl substitution reaction

A

The nucleophile attacks, opening the carbonyl and forming a tetrahedral intermediate –> The carbonyl then reforms, kicking off the leaving group
(The reaction is favored by acidic or basic conditions)

370
Q

Can carboxylic acids be reduced by sodium borohydride?

A

No

371
Q

Under what conditions will a carboxylic acid spontaneously decarboxylate?

A

1,3-dicarboxylic acids will spontaneously decarboxylate when heated, due to the stable cyclic intermediate step

372
Q

Cyclic form of amide

A

Lactam

373
Q

Cyclic form of ester

A

Lactone

374
Q

Cyclic form of anhydride

A

Anhydride

375
Q

Nucleophilic acyl substitution

A

The substitution of an attacking nucleophile for the leaving group of an acyl compound, which includes carboxylic acids, amides, esters and anhydrides

376
Q

Is nucleophilic acyl substitution favored under basic or acidic conditions?

A

Both

377
Q

Can carboxylic acids be reduced by lithium aluminum hydride?

A

Yes, they get reduced to primary alcohols

378
Q

Carboxylic acid

A

Contains a carbonyl and a hydroxyl group connected to the same carbon

379
Q

Are carboxylic acids terminal groups?

A

Yes

380
Q

Carboxylic acid suffix

A

-oic acid

381
Q

Salts suffix

A

-oate

382
Q

Dicarboxylic acid suffix

A

-dioic acid

383
Q

Physical properties of carboxylic acids

A

Polar
Participate in hydrogen bonding
Have high boiling points due to the hydrogen bonding
Exist as dimers in solution
Their acidity is enhanced by the resonance between the oxygen atoms
Their acidity can be enhanced by substituents that are electron-withdrawing
Their acidity can be decreased by substituents that are electron-donating

384
Q

Beta-dicarboxylic acids

A

Like other 1,3 dicarbonyl compounds, they have am alpha-hydrogen that is also highly acidic

385
Q

Are carboxylic acids polar or non-polar?

A

Polar

386
Q

Can carboxylic acids participate in hydrogen bonding?

A

Yes

387
Q

Do carboxylic acids have high boiling points?

A

Yes

388
Q

Why do carboxylic acids have high boiling points?

A

Because they can form hydrogen bonds

389
Q

How do carboxylic acids exist in solution?

A

As dimers

390
Q

How do carboxylic acids gain their acidity?

A

By the resonance between the oxygen atoms and by adding electron-withdrawing substituents to the compound. The closer the substituent is to the carbonyl carbon, the more acidic the compound will be.

391
Q

How can carboxylic acids’ acidity be reduced?

A

By adding electron-donating substituents to the compound. The closer the substituent is to the carbonyl carbon, the less acidic the compound will be.

392
Q

How can carboxylic acids be made?

A

By the oxidation of primary alcohols or aldehydes using an oxidizing agent like potassium permanganate (KMnO4)m dichromate salted (Na2Cr2O7 or K2Cr2O7) or chromium trioxide (CrO3)

393
Q

What is the product of nucleophilic acyl substitution if the nucleophile is an amine?

A

Amide

394
Q

What is the product of nucleophilic acyl substitution if the nucleophile is an alcohol?

A

Ester

395
Q

What is the product of nucleophilic acyl substitution if the nucleophile is another carboxylic acid?

A

Anhydride

396
Q

How can a carboxylic acid be reduced to a primary alcohol?

A

Strong reducing agents like lithium aluminum hydride (LiAlH4)

397
Q

Is sodium borohydride (NaBH4) strong enough to reduce a carboxylic acid to a primary alcohol?

A

No

398
Q

Which species can undergo spontaneous decarboxylation when heated?

A

Beta-dicarboxylic acids and other beta-keto acids

399
Q

Decarboxylation

A

Beta-dicarboxylic acids and other beta-keto acids are heated and lose a carbon as carbon dioxide

400
Q

What is the intermediate in a decarboxylation reaction?

A

A six-membered cyclic intermediate

401
Q

Saponification

A

Mixing of long-chain carboxylic acids (fatty acids) with a strong base, resulting in the salt we call soap

402
Q

Soap

A

Contain a hydrophilic carboxylate head and hydrophobic alkyl chain tail
Organize in hydrophilic environments to form micelles

403
Q

Micelle

A

Dissolves non polar organic molecules in its interior and can be solvated with water due to its exterior shell of hydrophilic groups

404
Q

Jones reagent

A

Chromium trioxide in aqueous sulfuric acid

405
Q

Is the Jones reagent oxidizing or reducing?

A

Oxidizing

406
Q

Is the Jones reagent a strong or weak oxidant?

A

Strong

407
Q

Esterification

A

Using an acid catalyst, the nucleophilic oxygen of an alcohol attacks the electrophilic carboxyl carbon of a carboxylic acid, ultimately displacing water to form an ester

408
Q

Is the alpha-hydrogen of a carboxylic acid more or less acidic than the hydroxyl hydrogen?

A

Less

409
Q

What kind of reaction occurs when a carboxylic acid reacts with ammonia to form an amide?

A

Condensation

410
Q

What is the byproduct of amide formation through reacting carboxylic acids with ammonia?

A

Water

411
Q

Condensation reaction

A

Two molecules are joined with the loss of a small molecule, like water

412
Q

What is responsible for the increased rate of hydrolysis in beta-lactams?

A

Beta-lactams are susceptible to hydrolysis due to the high level of ring strain, which is due to both torsional strain (eclipsing interactions) and angle strain (deviation from 109.5 degrees)

413
Q

What properties account for the differences in reactivity seen between anhydrides, esters and amides with nucleophiles?

A

Electronic effects like induction have some effect on the reactivity of carbonyl in these three functional groups. Differences in resonance also explain the increased reactivity of anhydrides, in particular. Steric effects could also be significant, depending on the specific leaving group present.

414
Q

Torsional strain

A

Comes from eclipsing interactions

415
Q

Angle strain

A

Comes from deviation from 109.5 degrees

416
Q

In the formation of an amide from ammonia and an anhydride, what serves as the nucleophile?

A

Ammonia

417
Q

In the formation of an amide from ammonia and an anhydride, what serves as the electrophile?

A

One of the carbonyl carbons of the anhydride

418
Q

Transesterification

A

The exchange of one esterifying group for another in an ester
Requires an alcohol as a nucleophile

419
Q

How do strongly acidic conditions catalyze the hydrolysis of an amide?

A

Catalyze amide hydrolysis by protonating the oxygen in the carbonyl
This increases the electrophilicity of the carbon, making it more susceptible to nucleophilic attack

420
Q

How do strongly basic conditions catalyze the hydrolysis of an amide?

A

Greatly increase the concentration of OH-, which can act as a nucleophile on amide carbonyls

421
Q

How are lactams named?

A

By the Greek letter of the carbon forming the bond with the nitrogen

422
Q

Fischer esterification reaction

A

The condensation of carboxylic acids with alcohols to form esters

423
Q

How are lactones named?

A

By the number of carbons in the ring and the Greek letter of the carbon forming the bond with the oxygen

424
Q

Triacylglycerols

A

A form of fat storage

Include 3 ester bonds between glycerol and fatty acids

425
Q

Steric hindrance

A

When a reaction cannot proceed (or is significantly slowed) because of substituents crowding the reactive site

426
Q

Protecting groups

A

E.g. acetals

Are used to increase steric hindrance or otherwise decrease the reactivity of a particular portion of a molecule

427
Q

Induction

A

Uneven distribution of charge across a sigma bond because of differences in electronegativity
The more electronegative groups in a carbonyl-containing compound, the greater its reactivity

428
Q

Resonance

A

Experienced through unhybridized p-orbitals, increasing stability

429
Q

Why are conjugated carbonyl-containing compounds more reactive?

A

Because they can stabilize their transition states

430
Q

Would increasing strain in a molecule make it more or less reactive?

A

More

431
Q

What causes ring strain?

A

Torsional strain (eclipsing interactions) and angle strain (deviation from 109.5 degrees)

432
Q

Which carboxylic acid derivatives cannot under nucleophilic substitution reactions?

A

None

433
Q

How can anhydrides be cleaved?

A

By the addition of a nucleophile

434
Q

Anhydride + ammonia

A

Amide + carboxylic acid

435
Q

Anhydride + amine

A

Amide + carboxylic acid

436
Q

Anhydride + alcohol

A

Ester + carboxylic acid

437
Q

Anhydride + water

A

Two carboxylic acids

438
Q

How can amides be hydrolyzed to carboxylic acids?

A

Under strongly acidic or basic conditions, where the attacking nucleophile is water or a the hydroxide anion

439
Q

Why should esterification reactions not be carried out in water?

A

Water molecules would hydrolyze the desired products back into the parent carboxylic acid

440
Q

What makes glycine unique among the amino acids?

A

All amino acids, except glycine, have chiral alpha-carbons. Because the R group of glycine is a hydrogen atom, it is not chiral and therefore is not optically active.

441
Q

What functional groups make amino acids amphoteric?

A

Carboxylic acids give amino acids their acidic properties because they can be deprotonated
Amino groups give amino acids their basic properties because they can be protonated

442
Q

How are peptide bonds formed?

A

A condensation reaction, in which water is lost

443
Q

How are peptide bonds cleaved?

A

Hydrolytic reaction with a strong acid or base

444
Q

Why is the C-N bond of an amide planar?

A

It has partial double-bond character due to resonance, making it planar
Double bonds exist in a planar conformation and restrict movement

445
Q

What are the four reactants in the Strecker synthesis of an amino acid?

A

Aldehyde, ammonium chloride (NH4Cl), and potassium cyanide (KCN) are used to make the aminonitrile; water is used to hydrolyze the aminonitrile to form the amino acid.

446
Q

What are the reaction types used in the Strecker synthesis?

A

Streicher synthesis is a condensation reaction (formation of an imine from a carbonyl-containing compound and ammonia, with loss of water), follow by nucleophilic addition *addition of the nitrile group), follow by hydrolysis

447
Q

What are the four main reactants in the Gabriel synthesis of an amino acid?

A

Gabriel synthesis begins with potassium phthalimide and diethyl bromomalonate, followed by an alkyl halide. Water is then used to hydrolyze the resulting compound to form the amino acid. While acid and bases are used at various times as catalysts, they are not main reactants.

448
Q

What are the reaction types used in the Gabriel synthesis?

A

Gabriel synthesis proceeds through two SN2 reactions, hydrolysis and decarboxylation

449
Q

What characteristics make inorganic phosphate so useful for energy transfer biologically?

A

It contains a very negative charge
When bonded to other phosphate groups in a nucleotide triphosphate, this creates repulsion with adjacent phosphate groups, increasing the energy of the bond
It can be resonance stabilized

450
Q

What is an organic phosphate?

A

Carbon-containing molecule with phosphate group (e.g. DNA, ATP, GTP)

451
Q

What characteristics of phosphoric acids make them good buffers?

A

The three hydrogens in phosphoric acid have very different pKa values. This allows phosphoric acid to pick ip or give off protons in a wide pH range, making it a good buffer over most of the pH scale

452
Q

What is the alpha carbon of an amino acid attached to?

A

An amino group, a carboxyl group, a hydrogen atom and an R group
It is a chiral center (except in glycine)

453
Q

Are eukaryotic amino acids L-amino acids or D-amino acids?

A

L-amino acids

454
Q

Do eukaryotic amino acids have (S) stereochemistry or (R) stereochemistry?

A

(S) stereochemistry (except cysteine is (R))

455
Q

All eukaryotic amino acids have (S) stereochemistry, except:

A

Cysteine

456
Q

How do amino acids exist in neutral solution?

A

As zwitterions

457
Q

Zwitterions

A

Dipolar ions

458
Q

Nonpolar, nonaromatic amino acids

A

Glycine, alanine, valine, leucine, isoleucine, methionine and proline

459
Q

Nonpolar, aromatic amino acids

A

Tryptophan and phenylalanine

460
Q

Polar, aromatic amino acids

A

Tyrosine

461
Q

Polar, nonaromatic amino acids

A

Serine, threonine, asparagine, glutamine and cysteine

462
Q

Negatively charged (acidic) amino acids

A

Aspartic acid and glutamic acid

463
Q

Positively charged (basic) amino acids

A

Lysine, arginine and histidine

464
Q

Polypeptides

A

Made up of multiple amino acids linked by peptide bonds

465
Q

Proteins

A

Large, folded, functional polypeptides

466
Q

Strecker synthesis

A

Generates an amino acid from an aldehyde

  1. An aldehyde is mixed with ammonium chloride (NH4Cl) and potassium cyanide (KCN)
  2. The ammonia attacks the carbonyl carbon, generating an imine
  3. The imine is then attacked by cyanide, generating aminonitrile
  4. The amininitrile is hydrolyzed by two equivalents of water, generating an amino acid
467
Q

Gabriel synthesis

A

Generates an amino acid from potassium phtbalimide, diethyl bromomalonate and an alkyl halide

  1. Phthalimide attacks the diethyl bromomalonate, generating a phthalimidomalonic ester
  2. The pthalimidomalonic ester attacks an alkyl halide, batting an alkyl group to the ester
  3. The product is hydrolyzed, creating pthalic acid (with two carboxyl groups) and converting the esters into carboxylic acids
  4. One carboxylic acid of the resulting 1,3-dicarbonyl is removed by decarboxylation
468
Q

Inorganic phosphate (Pi)

A

A buffered mixture of hydrogen phosphate (HPO4^2-) and dihydrogen phosphate (H2PO4-)

469
Q

What forms the backbone of DNA?

A

Phosphorus in phosphodiester bonds

470
Q

How are phosphodiester bonds formed?

A

A pyrophosphate (PPi, P2O7^4-) is released and pyrophosphate can then be hydrated to two inorganic phosphates

471
Q

Which amino acids contain sulfur?

A

Cysteine and methionine

472
Q

Can Strecker synthesis result in an optically active solution?

A

No, because it contains a planar intermediate that can be attacked from either side by a nucleophile, resulting in a racemic mixture of enantiomers and the solution will therefore be optically inactive

473
Q

Can Gabriel synthesis result in an optically active solution?

A

No, because it contains a planar intermediate that can be attacked from either side by a nucleophile, resulting in a racemic mixture of enantiomers and the solution will therefore be optically inactive

474
Q

What does infrared (IR) spectroscopy measure?

A

The absorption of infrared light by specific bonds, which vibrate. These vibrations cause changes in the dipole moment if the molecule that can be measured.

475
Q

What is IR spectroscopy generally used for?

A

The presence of functional groups to determine the identity of a molecule

476
Q

What two peaks would you expect to see in the IR spectrum of a carboxylic acid?

A

Broad O-H peak (2800 - 3200 1/cm)

Sharp carbonyl peak (1700 - 1750 1/cm)

477
Q

What types of molecules can be detected by UV spectroscopy?

A

Molecules with pi or nonbonding electrons and conjugated systems

478
Q

HOMO in UV spectroscopy

A

Highest occupied molecular orbital

479
Q

LUMO in UV spectroscopy

A

Lowest unoccupied molecular orbital

480
Q

In UV spectroscopy, how are HOMO and LUMO related to the absorption wavelength?

A

The smaller the difference in energy between HOMO and LUMO, the longer the wavelengths that can be absorbed by the molecule

481
Q

What does nuclear magnetic resonance (NMR) spectroscopy measure?

A

NMR measures alignment of the spin of a nucleus with an applied magnetic field

482
Q

What is NMR spectroscopy generally used for?

A

Identifying the different types and magnetic environments of protons in a molecule, which allows us to infer the connectivity (backbone) of a molecule

483
Q

What are the units for chemical shift on a standardized NMR spectrum?

A

Parts per million (ppm)

484
Q

What does it mean for a proton to be deshielded?

A

Deshielding occurs in molecules that have electronegative atoms that pull electron density away from the hydrogens being measured

485
Q

How does proton deshielding affect its peak in NMR spectroscopy?

A

Downfield (leftward) shift of the proton peak

486
Q

Spin-spin coupling

A

Occurs when two protons close to one another have an effect on the other’s magnetic environment. This results in the splitting of peaks into doublets, triplets or multiplets, depending on the environment

487
Q

Infrared (IR) spectroscopy

A

Measures absorption of infrared light, which causes molecular vibration (stretching, bending, twisting and folding)

488
Q

How are IR spectra plotted?

A

Percent transmittance v. wavenumber (1 / lambda)

489
Q

What is the normal range of an IR spectrum?

A

4000 to 400 1/cm

490
Q

Where is the fingerprint region of an IR spectrum?

A

1500 to 400 1/cm

491
Q

Fingerprint region of IR spectrum

A

1500 to 400 1/cm

Contains a number of peaks that can be used by experts to identify the compound

492
Q

How would a functional group appear on an IR spectrum?

A

Vibration of a bond must change the double bond moment

493
Q

O-H peak on IR spectrum

A

Broad

3300 1/cm

494
Q

OH peak of a carboxylic acid on IR spectrum

A

Broad

3000 1/cm

495
Q

N-H peak on IR spectrum

A

Sharp

3300 1/cm

496
Q

C=O peak on IR spectrum

A

Sharp

1750 1/cm

497
Q

Ultraviolet (UV) spectroscopy

A

Measures absorption of ultraviolet light, which causes movement of electrons between molecular orbitals

498
Q

How are UV spectra plotted?

A

Percent transmittance or absorbance v. wavelength

499
Q

How would a molecule appear on a UV spectrum?

A

It must have small enough energy difference between its highest occupied molecular orbital (HOMO) and its lowest unoccupied molecular orbital (LUMO) to permit an electron to move from one orbital to the other

500
Q

Conjugation

A

Occurs in molecules with unhybridized p-orbitals

501
Q

How does conjugation change a UV spectrum?

A

It shifts the absorption spectrum to higher maximum wavelengths (i.e. lower frequencies)

502
Q

Nuclear magnetic resonance (NMR) spectroscopy

A

Measures alignment of nuclear spin with an applied magnetic field, which depends on the magnetic environment of the nucleus itself

Nuclei may be in the lower-energy alpha-state or higher-energy beta-state; radio frequency pulses push the nucleus from the alpha-state to the beta-state, and these frequencies can be measured

503
Q

How are NMR spectra plotted?

A

Frequency v. absorption of energy

They are standardized by using chemical shift (delta)

They are calibrated during tetramethylsilane (TMS)

504
Q

What is the chemical shift of TMS?

A

0 ppm

505
Q

Where are higher chemical shifts located on an NMR spectrum?

A

Downfield (to the left)

506
Q

Where are lower chemical shifts located on an NMR spectrum?

A

Upfield (to the right)

507
Q

Integration on NMR

A

Area under the curve

Proportional to the number of protons contained under this peak

508
Q

How is a proton’s (or group of protons’) peak split?

A

n + 1 subpeaks

n = the number of protons that are three bonds away from the proton of interest

509
Q

Splitting patterns

A

Doublets, triplets and multiplets

Occur due to coupling between protons on adjacent carbon atoms

510
Q

Where are protons on sp3-hybridized carbons located on NMR?

A

0 to 3 ppm range

511
Q

Where are protons on sp2-hybridized carbons located on NMR?

A

4.6 to 6.0 ppm range

512
Q

Where are protons on sp-hybridized carbons located on NMR?

A

2.0 to 3.0 ppm range

513
Q

Where are aldehydes located on NMR?

A

9 to 10 ppm range

514
Q

Where are carboxylic acids located on NMR?

A

10.5 to 12 ppm range

515
Q

Where are aromatic hydrogens located on NMR?

A

6.0 to 8.5 ppm range

516
Q

In an IR spectrum, how does extended conjugation of double bonds affect the absorbance band of carbonyl (C=O) stretches compared with normal absorption?

A

The absorbance band will occur at a lower wavenumber

Carbonyl groups in conjugation with double bonds tend to absorb at lower wavenumber because the delocalization of pi electrons causes the C=O bond to lose double bond character, shifting the stretching frequency closer to C-O stretches. Remember that higher-order bonds tend to have higher absorption frequencies, so loss of double-bond character should decrease the absorption frequency of the group.

517
Q

Coupling constant (J)

A

A measure of the degree of splitting caused by other atoms in the molecule

518
Q

The IR spectrum of a fully protonated amino acid would likely contain:

A

A sharp peak at 1750 1/cm and a sharp peak at 3300 1/cm

519
Q

What must be true about the two solvents used for an extraction to work?

A

The two solvents must be immiscible and must have different polarity or acid-base properties that allow a compound of interest to dissolve more easily in one than the other

520
Q

When doing an extraction, would it be better to do three extractions with 10 mL of solvent, or one extraction with 30 mL?

A

It is better to do three washes with 10 mL than to do one with 30 mL; more of the compound of interest would be extracted with multiple sequential extractions than one large one

521
Q

Would acid dissolve better in aqueous acid or aqueous base?

A

Acid dissolves better in aqueous base because it will dissociate to form the conjugate base and, being more highly charged, will become more soluble.

Note that like dissolves like applies to polarity; acids and bases dissolve more easily in solutions with the opposite acid-base characteristics.

522
Q

Distillation separates compounds based on what property?

A

Differences in boiling points

523
Q

If we are given a solution of ether, with a boiling point of 308 K, and methylene chloride, with a boiling point of 313 K, which type of distillation should be used to separate them?

A

Fractional distillation

524
Q

If we are given a solution of bromobenzene, with a boiling point of 156 C, and camphor, with a boiling point of 204 C, which type of distillation should be used to separate them?

A

Vacuum distillation because the chemicals have very high boiling points and the decreased ambient pressure will allow them to boil at a lower temperature

525
Q

What properties of molecules do thin-layer chromatography, paper chromatography and standard column chromatography take advantage of to separate compounds?

A

Charge and polarity

526
Q

Types of column chromatography

A

Ion-exchange, size-exclusion, and affinity

527
Q

In what way is gas chromatography distinct from all of the other techniques of chromatography?

A

The same technique of mobile and stationary phases are performed with a gaseous eluent (instead of liquid). The stationary phase is usually a crushed metal or polymer.

528
Q

What is the major historical distinction between HPLC and column chromatography?

A

HPLC was performed at high pressures, whereas column chromatography uses gravity to pill the solution through the column

529
Q

What is the major modern distinction between HPLC and column chromatography?

A

HPLC is performed with sophisticated and variable solvent and temperature gradients, allowing for much more specific separation of compounds than column chromatography. High pressures are no longer required.

530
Q

Ion-exchange column chromatography

A

Column is given a charge, which attracts molecules with the opposite charge

531
Q

Size-exclusion column chromatography

A

Small pores are used; smaller molecules are trapped, while larger molecules pass through the column

532
Q

Affinity column chromatography

A

Specific receptors or antibodies can trap the target in the column; the target must then be washed out using other solutions

533
Q

Retardation factor (Rf)

A

= (distance spot moved) / (distance solvent front moved)

534
Q

Extraction

A

Combines two immiscible liquids, one of which easily dissolves the compound of interest
Carried out in a separatory funnel : one phase is collected, and the solvent is then evaporated
Acid-base properties can be used to increase solubility

535
Q

Aqueous phase

A 
The polar (water) layer
Dissolves compounds with hydrogen bonding or polarity
536
Q

Organic phase

A

The nonpolar layer

Dissolves nonpolar compounds

537
Q

Wash

A

The reverse of extraction

A small amount of solute that dissolves impurities is run over the compound of interest

538
Q

Filtration

A

Isolates a solid (residue) from a liquid (filtrate)

539
Q

Gravity filtration

A

Used when the product of interest is in the filtrate

Hot solvent is used to maintain solubility

540
Q

Vacuum filtration

A

Used when the product of interest is the solid

Vacuum is connected to the flask to pull the solvent through more quickly

541
Q

Recrystallization

A

The product is dissolved in a minimum amount of hot solvent. If the impurities are more soluble, the crystals will reform while the flask cools, excluding the impurities.

542
Q

Distillation

A

Separates liquids according to differences in their boiling points; the liquid with the lowest bolding point vaporizes first and is collected as the distillate

543
Q

Simple distillation

A

Can be used if the boiling points are under 150 C and are at least 25 C apart

544
Q

Vacuum distillation

A

Should be used if the boiling points are over 150 C to prevent degradation of the product

545
Q

Fractional distillation

A

Should be used if the boiling points are less than 25 C apart because it allows more refined separation of liquids by boiling point

546
Q

Chromatography

A

Uses two phases to separate compounds based on physical or chemical properties

547
Q

Stationary (absorbent) phase

A

Usually a polar solid

548
Q

Mobile phase

A

Runs though the stationary phase and is usually a liquid or gas
Elutes the sample though the stationary phase

549
Q

Do compounds with a higher affinity for the stationary phase have smaller or larger retardation factors?

A

Smaller

Therefore, they take longer to pass through, if at all

550
Q

Partitioning

A

Separating compounds in chromatography, but having one stick to the stationary phase due to its higher affinity for it, while the other one passing through the stationary phase due to its high affinity to the mobile phase

551
Q

Thin-layer and paper chromatography

A

Used to identify a sample
The card is spotted and developed
Rf values can be calculated and compared to reference values

552
Q

What is the stationary phase in thin-layer and paper chromatography?

A

Polar material, such as silica, alumina or paper

553
Q

What is the mobile phase in thin-layer and paper chromatography?

A

Nonpolar solvent, which climbs the card though capillary action

554
Q

Reverse-phase chromatography

A

Uses a nonpolar card with a polar solvent

555
Q

Column chromatography

A

Utilizes polarity, size, or affinity to separate compounds based on their physical or chemical properties

556
Q

What is the stationary phase in column chromatography?

A

Silica or alumina beads

557
Q

What is the mobile phase in column chromatography?

A

Nonpolar solvent, which travels though the column by gravity

558
Q

Gas chromatography

A

Separates vaporizable compounds according to how well they adhere to the adsorbent in the column
Can be combined in sequence with mass spectrometry, which ionizes and fragments molecules and passes these fragments through a magnetic field to determine molecular weight or structure

559
Q

What is the stationary phase in gas chromatography?

A

Crushed metal or a polymer

560
Q

What is the mobile phase in gas chromatography?

A

Nonreactive gas

561
Q

High-performance liquid chromatography (HPLC)

A

Similar to column chromatography but uses sophisticated computer-mediated solvent and temperature gradients. It is used if the sample side is small or if forces such as capillary action will affect results. It was formerly called high-pressure liquid chromatography

MCAT (7 decks)

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