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Flashcards in Orgo Deck (143):
1

What is a lactone?

circularized ester

2

What is a lactam?

circularized amide

3

What is another word for alkene?

olefin

4

What is another word for epoxide?

oxirane

5

What is another cyanohydrin?

carbon bonded to an alcohol and a CN

6

How are substituents ordered in a compound name?

in alphabetical order, not including the prefixes i.e. di, tri etc

7

How are compounds named when there is an alcohol in them?

so that lowest priority is given to the alcohol

8

What is the formula for unsaturation?

(2n + 2 + N - X - H) / 2

9

What are some general trends for electron donating groups?

alkyl groups i.e. CH3, Et etc
lone pair groups/atoms

10

What are some general trends for electron withdrawing groups?

halides
no lone pair
ie NO2

11

When does resonance stabilization occur?

in a conjugated system with 3 or more atoms that each have a p orbital

12

What are the 3 rules for resonance structures?

1) resonance structures can never be drawn through atoms that are truly spy hybridized
2) usually only involve electrons that are adjacent to a pi bond or an unhybridized p orbital
3) resonance structures of lowest energy are the most important

13

What 3 main criteria does evaluation of resonance structure rely on?

1) contributors in which the octet rule is satisfied for all toms are more important than for ones in which its not
2) contributors that minimize separation charge (formal charge) are better
3) if there are formal charges negatives should be on the more electronegative atoms and positives on the less electronegative atoms

14

What is a Bronsted-Lowry acid?

molecule that can donate a proton

15

Rank the stability of a carbocation from most to least stable

3 > 2 > 1 > Me

16

Rank the stability of a carbanion from most to least stable

Me > 1 > 2 > 3

17

What is a Bronstad-Lowry base?

accepts protons

18

What is a Lewis acid?

electron acceptor

19

What is a Lewis base?

electron donator

20

In general what is the order of relative acidity for organic compounds?

strong acids
sulfonic acids
carboxylic acids
phenols
alcohols and water
aldehydes and ketons
sp CH
sp2 CH
sp3 CH

21

What are the 6 strong acids (for the MCAT)?

HClO4
H2SO4
HNO3
HCl
HBr
HI

22

How do inductive effects affect acidity?

the closer an electron-withdrawing group is to the acidic proton, the greater the stabilizing effect and thus the greater the acidity
closer = better
more electronegative = better
electron-donating groups tend to destabilize and thus decrease acidity

23

Are nucleophiles Lewis acids or bases?

Lewis bases because they donate electrons

24

Are electrophiles Lewis acids or bases?

Lewis acids because they accept electrons

25

What are the general trends for nucelophilicity?

1) increases as negative charge increases
2) increases going down a group (larger, more polarizable)
3) increases going left across a period (less electronegative)

26

What is polarizability?

how easy it is for the electrons surrounding an atom to be distorted
generally down a group atoms become larger and more polarizable

27

What are some characteristics of a good leaving group?

weak C-LG bond (electronegative atoms or EWGs)
stable and unreactive products (low basicity, stable from resonance etc, large)

28

What is a better leaving group R-OH or R-OMs?

R-OMs

29

What is more reactive, a C-C double bond or a strained carbon ring?

C-C double bond

30

Do cyclopentane and cyclohexane undergo hydrogenation reactions under normal conditions?

no, they are relatively-strain free compared to smaller hydrocarbon rings

31

What are constitutional isomers?

same formula, different structure

32

What are conformational isomers?

same formula, same connectivity, different sigma bond rotation
ie eclipsed and staggered conformations

33

What are stereoisomers?

same formula, same connectivity, different 3D arrangements that cannot be changed by rotation of sigma bonds

34

If a compound rotates plane polarized light clockwise what is it classified as?

dextrorotatory
+

35

If a compound rotates plane polarized light counter clockwise what is it classified as?

levorotatory
-

36

When assigning absolute configuration how does priority work among isotopes?

assigned based on atomic weight
highest weight = highest priority

37

What are enantiomers?

non-superimposable mirror images
have the opposite absolute configuration at all chiral centres
have many identical physical properties
rotate plane polarized light in opposite directions (same magnitude)

38

What are diastereomers?

stereoisomers that aren't enantiomers
opposite absolute configuration at some chiral centres i.e. only one needs to be the same
physical and chemical properties can vary dramatically
specific rotation is different, but there is no relationship between them

39

What are mess compounds?

need to have an even number of chiral centres and a line of symmetry
optically inactive
have chiral centres but are achiral

40

Do stereoisomers include E/Z configurations?

yes

41

How are enantiomers separated?

resolution
attach chiral probes which make them diasteromers than separate based on their different physical properties then release the probe

42

What are geometric isomers?

a type of diasteromers
have different orientation around a ring or double bond
cis/trans (for double bonds or rings)
E/Z (only for double bonds)

43

What are epimers?

diasteromers that are opposite at only one chiral centre
ie L-glucose and D-glucose

44

What are anomers?

ring formations of epimers (which are diastereomers)
ie alpha-glucose and beta-glucose

45

What is the mobile phase in chromatography usually for?

it is usually a solvent and the mix to be separated

46

What is the stationary phase in chromatography usually for?

its usually something that the mix to be separated interacts with

47

What are the 4 options for the force driving the mobile phase in chromatography?

capillary action
gravity
pressure
magnet

48

What are the 5 physical properties used to separate compounds in chromatography? Will they work for enantiomer separation?

polarity
size
charge
specific affinity
volatility
no they won't differ for enantiomers because they are physical properties

49

What is the stationary phase in thin layer chromatography?

silica (SiO2) coated glass plate (polar)

50

Which compounds move farthest in thin layer chromatography? Do they have a high or low Rf?

nonpolar compounds move farther than polar ones
they have a higher Rf

51

Explain column/flash chromatography

kind of like TLC using gravity and a column
column is filled with glass beads coated in silica (SiO2)
mixture of compounds to be separated are poured in and extra solvent is added periodically
compounds are collected at the bottom
nonpolar compounds come out first
polar compounds come out later because they interact with the silica

52

Explain size-based exclusion chromatography

large porous beads line a column
solvent with mixture is poured into the top
small molecules take a longer path so they come out later
large molecules take a shorter path and therefore come out first
used for separating polymers and monomers etc

53

Explain ionic exchange chromatography

column is lined with resin that is functionalized with charged groups (entire column is either negative or positive) i.e. Na+SO4-
mobile phase containing the mixture to be separated is put through
as it passes through the positively charged groups will replace the Na+ while the negatively charged and neutral species will pass right through
column can then be eluted with a concentrated sodium-containing solution to displace all the positively charged species
frequently used for separating proteins

54

Explain affinity chromatography

usually used to purify proteins or nucleic acids from cell lysates etc
large scale: column is packed with resin and sample is poured in
smaller scale: solid phase is mixed with sample in a small tube then centrifuged
solid phase with protein of interest goes to the bottom and supernatant can just be decanted
magnetic beads can also be used instead and held by a magnet while the solution is decanted

55

How are proteins of interest isolated using affinity chromatography?

either an antibody specific for the protein of interest is added and then protein A, G or L linked to a solid support is added (bind mammalian antibodies)
or an affinity tag can be used
added to the N or C terminus
i.e. His tags are 6-10 histidine AAs and will bind ions of resin such as nickel
done under high pH and His-tagged proteins can then be eluted under low pH conditions

56

Describe generally how HPLC (high performance liquid chromatography) works

mobile phase is pressurized
it is then injected by a syringe and carried to the column (4 different types)
sample is separated into individual flasks by retention time
components are detected and analyzed by UV/vis or mass spectrometry as the exit the column
increases speed and efficiency

57

What are the 4 types of HPLC? Which is the most common?

normal phase
reverse phase
size exclusion
ion exchange
*reverse phase is the most common (assume if not indicated on mcat)

58

How does normal phase HPLC work?

mobile phase is less polar, stationary phase in more polar
nonpolar compounds come out first
*like TLC or column chromatography

59

How does reverse phase HPLC work?

mobile phase is more polar than stationary phase
polar compounds come out first
*remember to assume this if its not indicated

60

How does size exclusion HPLC work?

mobile phase is a solvent and stationary phase is porous beads
large compounds come out first

61

How does ion exchange HPLC work?

mobile phase is solvent
stationary phase is charged resin
same charge as resin and neutral compounds come out first

62

What is something important to take into consideration before using gas chromatography?

you lose all of your sample, so don't use it if you want the sample at the end

63

Explain how gas chromatography works

"separates" compounds based on their volatilities
sample is loaded and vaporized and carried along with an inert gas (usually helium)
moved through a column that has particles coated with liquid absorbent (viscous, high BP)
as components exit the column they are burned and a detector determines the number of components and their relative amounts
compounds with low volatility (high BP) move slowly because they turn to liquid or solid
compounds with high volatility (low BP) stay a gas and move faster (are out first)

64

What is fractional distillation?

usually used for liquids that have solid impurities
separates compounds with similar boiling points via volatility
column is packed with glass beads or steel sponge
mix is heated, boils, evaporates and condenses over and over and the vapour at the top becomes nearly purely the lower boiling component
it reaches the condenser (that uses cold water) and can then be collected as liquid

65

What is simple distillation?

used to eliminate trace impurities or separate compounds that have large boiling point differences
doesn't have a column, you just boil and condense what you want
is less specific

66

What are extractions used for?

separating a complex mix of organic molecules via solubility

67

What will be in the aqueous layer of an extraction to begin with?

inorganic salts
strong acids and bases
alcohols, amines and carboxylic acids that are less than 5C

68

What will move into the aqueous layer of an extraction if you add 5% NaHCO3?

weak acids will move in
(because HCO3 is a weak base and will deprotonate them)

69

What will move into the aqueous layer of an extraction if you add 10% NaOH?

very weak acids will move in
(because it is a stronger base and will deprotonate them)

70

What will move into the aqueous layer of an extraction if you add 5% HCl?

weak bases will move in
(because it is a strong acid and will deprotonate them)

71

What is generally left in the organic layer of an extraction at the end?

nonpolar compounds
(can be isolated by evaporation if the non polar compound was what you wanted)

72

How are enantiomers resolved?

use a resolving agent i.e. tartaric acid to create diastereomers which will have different physical properties
separate and the cleave off the tartaric acid

73

What is mass spectroscopy and what is it used for?

very specific
is used to find a molecule's molecular weight or formula
involves molecules being ionized by bombardment with electrons and then being put in an electric field

74

What is deuterium?

hydrogen that has an extra neutron and thus weighs 2

75

What is UV/vis spectroscopy and what is it used for?

used to study the structure of metals and conjugated organic molecules
the more conjugation the longer the wavelength of max absorption will be
shorter wavelength and higher energy than IR
usually for covalent bonds

76

What is IR spectroscopy and what is it used for?

used different wavelengths to vibrate covalent bonds in order to identify functional groups

77

What is IR spectroscopy data measured in?

wavenumber, which is indirectly proportional to wavelength and directly proportional to frequency and energy
usually graph goes from 1000 to 4000 cm^-1

78

What is usually found in the 600-1600cm^-1 range on IR data?

nothing useful, this is the fingerprint region

79

Where are CH bonds found in an IR?

spikes at 2800-3300 cm^-1

80

Where are C-C double bonds found in an IR?

1650 cm^-1

81

How does stiffness affect bond vibration in IR?

more stiff bonds resonate at higher frequencies

82

Where are C-C triple bonds found in an IR?

2200 cm^-1

83

How does atomic mass affect bond vibration in IR?

atoms with higher mass have lower frequency
ie C would be higher than O

84

Where are most common functional groups found on an IR?

1600-3500 cm^-1

85

Describe an OH on an IR graph

strong broad peak (because of H-bonding) from 3600-3200 cm^-1

86

Describe an NH bond on an IR graph

little bit wide, moderately strong peak from 3150-2500

87

Describe a carbonyl bond on an IR

strong spike around 1700

88

Describe an alkene on an IR

variably strong around 1650

89

Describe a CN triple bond on an IR

variably strong, around 2200

90

Describe a CC triple bond on an IR

variably strong, less strong than CN
around 2200

91

What is usually the difference between aliphatic and aromatic CH bonds on an IR?

aliphatic CH bonds are usually a little less than 3000
aromatic CH bonds are usually a little more than 3000

92

Where are CH bonds found in general in an IR?

3300-2700

93

Where are sp3 carbons on an IR?

3000-2850

94

Where are sp2 carbons on an IR?

3150-3000

95

Where are sp carbons on an IR?

3300

96

Which side is downfield on an NMR? Are these shielded or deshielded?

downfield is to the left
this is deshielded

97

What is HNMR for?

it uses light energy and absorption for the structural info of the hydrogens in a molecule

98

What does the number of peaks in an HNMR tell you?

the number of non-equivalent hydrogens

99

What is the area under a peak of an HNMR proportional to?

RELATIVELY proportional to the number of Hs of that type

100

What does splitting tell you on an HNMR?

# of non-equivalent H neighbours + 1

101

What do shift values on an HNMR tell you?

tell you about the environment of the H i.e. the shielding

102

What is shielding?

the electrons around an H make a magnetic field which shields it, therefore giving it more energy for absorption, moving it upfield

103

What is happening to a deshielded H?

electrons are being pulled away from it, creating less of a personal magnetic field
shifted downfield on an HNMR

104

What affect do heteroatoms have of Hs in an HNMR?

they block so you can only see Hs on one C away

105

What are heteroatoms?

any atom that isn't carbon or hydrogen

106

What affects the shielding of an H?

electronegativity of neighbouring atoms
hybridization
acidity and hydrogen bonding

107

How does acidity affect the shielding of Hs?

deshields them
acidic Hs are downfield on an HNMR

108

How does electronegativity of neighbouring atoms affect the shielding of Hs?

near electronegative atoms Hs are more deshielded

109

How does hybridization affect the shielding of Hs?

sp are most deshielded > sp2 > sp3 are the most shielded
(greater the s character the more deshielded)

110

Where are aldehyde Hs found on an HNMR?

9-10ppm

111

**Where are aromatic Hs found on an HNMR?

6.5-8

112

**Where are vinyl Hs found on an HNMR?

5-6

113

Where are halogen, beside an amine or beside an ether Hs found on an HNMR?

2.5-4

114

**Where are alkyl (normal) Hs found on an HNMR?

just above 0-2

115

Where are carboxylic acids Hs found on an HNMR?

10-13

116

Where are alcohol Hs found on an HNMR?

2-5

117

Where are benzylic Hs found on an HNMR?

2.5-3.5

118

Where are alkyne Hs found on an HNMR?

2

119

Name 6 oxidizing agents. What will they reduce alcohols to?

H2CrO4
CrO42-
Cr2O72-
MnO4-
CrO3
PCC
they will all reduce primary alcohols to carboxylic acids except for PCC (aldehyde)
they will all reduce secondary alcohols to ketones

120

What happens in a nucleophilic addition reaction?

pi bond is broken
2 sigma bonds are formed

121

Name 2 reducing agents. What do they usually do?

NaBH4
LiAlH4
usually add a hydride to a carbonyl, making an alcohol

122

What kind of solvent is used when using a Grignard reagent?

aprotic solvent (because they're very basic)

123

What are mesyls and tosyls used for?

protecting alcohols or amino groups
(have SO3- attached to some Cs)

124

What is used to form an imine?

weakly acidic conditions and an aldehyde or ketone with a primary amine

125

What is used to form an examine?

catalyzed with acid
aldehyde or ketone with a secondary amine
(can be reversed with aqueous acid)

126

What is an aldol condensation reaction?

when the enolate of one carbonyl compound reacts with the carbonyl of another carbonyl compound
forms a beta-hydroxycarbonyl compound
"crossed" when two different carbonyl compounds are used
requires strong acid

127

What is the thermodynamic control of aldol reactions?

use an unencumbered base and run at room temp
enolate is formed by removing protons from the more sterically crowded alpha-carbon

128

What is the kinetic control of aldol reactions?

use a bulky base and low temperatures
enolate is formed at the less substituted alpha-carbon

129

What two things can be done with the product of an aldol condensation reaction?

treat with a strong base to reverse the reaction (called a retro-aldol reaction)
or
undergo dehydration using heat to form an alpha,beta-unsaturdated carbonyl compound

130

How can carboxylic acids be reduced to primary alcohols?

using LiAlH4
(but NOT NaBH4)

131

Why are carboxylic acids that have carbonyl groups beta to the carboxylate unstable?

because they can undergo decarboxylation

132

What is acyl substitution?

also called nucleophilic addition-elimination reactions
a new pi bond is formed and 2 sigma bonds break
go through a tetrahedral intermediate

133

What is esterification?

carboxylic acid and alcohol react in the presence of a catalytic amount of acid to form an ester

134

What is saponification?

basica hydrolysis of a triacylglyceride
(get glycerol and 3 fatty acids)

135

What is used to make acid halides?

SOCl2 or PX3 (X= Br, Cl)

136

How is an acid anhydride made?

condensation of two carboxylic acids or addition of a carboxylic acid to an acid halide

137

Can amides be prepared directly from carboxylic acids?

no because they are very basic and will deprotonate the carboxylic acid first

138

Put the carboxylic acid derivatives in order of relative reactivity (most to least reactive)

acid chloride > acid anhydride > esters > amides

139

What is an SN2 mechanism?

only one step
"backside attack"
has a pentavalent transition state
product is inverted
rxn rate depends on both the nucleophile and electrophile
don't want bulky Nu, should be strong
less substituted substrates react faster than more substituted ones
methyl > 1 > 2 >> 3
use polar, aprotic solvents

140

What is an SN1 mechanism?

two steps
has a carbocation intermediate
3 > 2 > 1 > methyl
results in a racemic mixture
rxn rate only depends on electrophile (leaving group needs to leave)
use ptotic solvents (stabilize the carbocation)
non-basic, weaker Nu, often the solvent itself (solvolysis)

141

What is Strecker synthesis?

synthetic synthesis of amino acids using ammonium and cyanide salts
(goes through an imine)

142

What is Gabriel-malonic ester synthesis?

synthetic synthesis of amino acids using the N in pthalamide and an alpha-bromomalonic-ester

143

What is DCC coupling?

used for artificially synthesizing peptides
DCC converts the OH of the carboxylate group in an amino acid to a good leaving group