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1
Q

Which order are peptide sequences written?

A

N to C terminus

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2
Q

What is the 𝛼 carbon in an amino acid

A

Carbon to which the carboxylic acid is attached, can have L or D stereochemistry

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3
Q

What types of C terminus are there

A

Free C terminus = carboxylic acid
Capped C terminus = amide group

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4
Q

Monosaccharide

A

single sugar unit

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5
Q

Disaccharide

A

2 sugar units

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6
Q

Oligosaccharide

A

2+ sugar units

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7
Q

What is the anomeric carbon in a sugar unit

A

1st carbon from O atom

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8
Q

Glycoside

A

any carbohydrate molecule with an anomeric substituent other than OH

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9
Q

What is mutarotation?

A

When free monosaccharides equilibrate between the acyclic (open chain) and cyclic form - leading to a mixture of 2 stereoisomers where anomeric OH is either equatorial or axial.
Once a glycosidic bond forms no longer free for mutarotation, stereochem is fixed

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10
Q

Whats is the most stable conformer of most hexose sugars?

A

Chair conformation with the most substituents in equatorial position

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11
Q

Structure of glucose

A

All OH equatorial

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12
Q

Structure of Galactose

A

All OH equatorial apart from C4 ax.

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13
Q

Structure of Mannose

A

All OH equatorial apart from C2 ax.

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14
Q

Structure of GlcNAc

A

All equatorial OH apart from C2 which has axial NHCOCH3 group

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15
Q

How to achieve efficient and selective coupling between amino acids?

A

1) increase reactivity by activating C terminal COOH, better leaving group than OH
2) encourage regio/chemo selectivity by installing protecting groups
3) avoid loss of stereochemistry/ racemisation

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16
Q

What are the disadvantages of using acid chloride to activate COOH group of amino acid?

A

Causes racemisation of products
Intramolecular cyclisation of acid chloride subs amino acid forms oxazolone leading to keto-enol tautomerisation = chiral centre of amino acid to racemise

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17
Q

How to minimise racemisation when reacting amino acids?

A

Use a coupling reagent to activate the C terminus
Do C- to N- terminal peptide synthesis

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18
Q

Coupling reagents

A

DCC - after coupling forms a urea - insoluble so ppt out of solution and drives reaction
HATU
HBTU
HCTU

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19
Q

What must you consider when choosing a protecting group?

A

1) stability towards condition used in subsequent steps (acid/base)
2) orthogonality - any possible effects the conditions of removal may have on other protecting groups
3) selectivity - the ability to add to specific positions

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20
Q

Protecting groups for amines

A

Boc + base (DiPEA)
Fmoc + base (DiPEA)
Mechanism: Nucleophilic attack of NH2 to C=O of protecting group then deprotonation by base

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21
Q

How to protect w Boc group

A

Boc2O and DiPEA

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22
Q

How to deprotect Boc group

A

Acidic conditions (TFA)

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23
Q

How to protect with Fmoc

A

Fmoc-Cl and DiPEA

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24
Q

How to deprotect Fmoc

A

Basic conditions (piperidine)

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25
Protecting groups for carboxylic acids
Methyl ester Benzyl ester Allyl ester Tert-butyl ester
26
Protect w Methyl ester
MeOH and HCl
27
Deprotect Methyl ester
Aqueous hydrolysis w base NaOH + H2O
28
Protect with Benzyl ester
Bz-CH2-OH and HCl
29
Deprotect Benzyl ester
Pd/C + H2
30
Protect with allyl ester
HO-CH3CH2CH2 and HCl
31
Deprotect allyl ester
Pd(PPh3)4
32
Protect with tert-butyl ester
HOC(CH3)3 and HCl
33
Deprotect tert-butyl ester
Acid e.g. TFA
34
Protect hydroxyl side chain group
Tert butyl ether Benzyl ether Silyl ether
35
Protect with Benzyl ether
BnBr and NaH (to deprotonate alcohol grp)
35
Protect with tert butyl ether
HOC(CH3)3 and acid
36
Deprotect tert-butyl ether
Conc TFA or HCl
37
Deprotect benzyl ether
Pd/C H2
38
Protect with silyl ether
Me3Si-Cl and base
39
Deprotect silyl ether
TBAF
40
What is solid supported synthesis of peptides?
The construction of peptides on insoluble funtionalised polymer beads or resin Assemble peptide on N terminus end Peptide cleaved off after synthesis
41
Chloro methyl polystyrene resin
Resin-Ph-CH2-Cl
42
Wang resin
Resin-CH2-OH
43
Rink Amide resin
Resin- CH2- NH2
44
How to release peptides from the solid support
Generally under acidic conditions Usually solution of TFA in organic solvent
45
In solid phases synthesis N-terminal amine is generally protected with...
Fmoc instead of Boc as Boc is cleaved under acidic conditions so when trying to cleave Boc will also cleave peptide from solid support
46
What coupling reagents to use in solid phase synthesis?
Generally use DIC instead of DCC to avoid producing an insoluble urea byproduct which would ppt out of solution
47
How to chose side chain protecting groups when doing solid phase peptide synthesis
Choose groups where deprotection occurs simultaneously with release of peptide from solid support ( deprotect under acidic conditions e.g Boc, tBu)
48
As HF is toxic and corrosive what other acid is instead used for cleavage of peptides from resin
Usually solution of TFA in organic solvent
49
Challenges to gylcosidic bond formation. e.g between 2 glucose units
1) Reactivity OH is poor leaving group 2) Regioselectivity - which 2 carbons do we want to link 3) Stereoselectivity - glycosidic bond 𝛼 or β
50
How to achieve selective coupling between 2 monosaccharides?
1) increase donor reactivity by activating anomeric hydroxyl group by turning into better LG 2) install appropriate protecting groups on both donor and acceptor monosaccharides 3) Encourage stereoselectivity for 𝛼 or β by selecting appropriate PG or reaction conditions
51
For selective protection of the Primary Hydroxyl group
Tri Phenyl methyl ether Trityl-Cl + base
52
Deprotect Tri Phenyl methyl ether
Mild acid
53
Non-selective protecting groups
Acetyl esters (Ac2O + pyridine) Benzoyl esters
54
Deprotect Acetyl esters or benzoyl esters
NaOMe
55
Selective protection of 1,3- Diols
Benzylidene acetal Always added across C4-C6
56
Selective cleavage of benzylidene acetal from C6 Hydroxyl group
LiAlH4
57
Selective cleavage of benzylidene acetal from C4 Hydroxyl group
NaBH4
58
How to activate anomeric hydroxyl group
Install good leaving group, X, at anomeric position - results in formation of reactive intermediate oxocarbenium ion
59
Good leaving groups at anomeric carbon
Bromide (activated with Ag2CO3) Trichloroacetimidate CCl3CN (Activated by Lewis acid TMSOTf) Thioethers
60
How to attach Br to anomeric position
Ac2O + pyridine HBr
61
How to attach CCl3CN to anomeric position
CCl3CN + NaH then activated by TMSOTf
62
How to attach a thioether to anomeric position
HBr Ph-SH Ag2CO3
63
How to control stereochemistry of the glycosidic bond?
1) the anomeric effect (more 𝛼 than β product) 2) neighbouring group participation 3) Choice of solvent 4) Reactivity of the acceptor
64
Explanation of the anomeric effect in glycosidic bond formation
1) dipole minimisation - when the 𝛼 anomer formed the dipoles of the 2 oxygens point in opposite directions whereas in β they are partially aligned = unfavourable 2) hyperconjugation - in 𝛼 anomer there is orbital overlap between axial lone pair on cyclic O and the antibonding orbital of axial C-O bond = stabilising
65
Explanation of Neighbouring group participation in glycosidic bond formation
If C2 OAc group in eq will form β as major product but if C2 OAc in ax will form 𝛼 as major product
66
Explanation of solvent effects in forming glycosidic bonds
Nucleophilic solvents can participate in the reaction giving "glycosated' solvent adducts. Act as intermediates for further reaction with the acceptor via SN2 subs = inversion of stereochem
67
Why do strong nucleophiles used to form glycosidic bond go against anomeric effect?
Because the stronger nucleophiles go through an SN2 like substitution where the oxocarbenium ion doesnt fully form so just inverts stereochemistry

ACCA 3 (4 decks)

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