Biological molecules

Common protection methods for N-terminus of an amino acid (general) (2)

Boc (Boc2O) + base, Fmoc-Cl + base

How to deprotect Boc

TFA F3C-COOH

How to deprotect Fmoc

piperidine

Common protecting groups of the carboxylic acid of the C-terminus (general) (4)

generally esterification with an alcohol (MeOH + HCl(methyl ester)/ Bn-COH+ HCl(benzyl ester)/ allyl ester/ tert-butyl ester)

How to deprotect the methyl ester

NaOH, H2O

how to deprotect the benzyl ester/ether

H2/ Pd/C

how to deprotect the allyl ester

Pd(PPh3)4

how to deprotect tert-butyl ester/ether?

TFA

common methods to protect hydroxyl groups (3)

tert-butyl ether, benzyl ether, silyl ether

How to deprotect a silyl ether

TBAF

Whats the issue with activating the C-terminus as an acid chloride

racemisation of the activated amino acid forming unwanted byproducts with the wrong stereochemistry caused by oxazolone formation

what do we use to activate the C- terminus and examples (2)

coupling reagent, DCC and HATU +base

How to selectively protect the anomeric OH

MeOH + HCl

How to selectively deprotect the anomeric OH?

H2NNH2 or benzyl amine

How to selectively protect the 1,3-diols?

Benzylidene acetal + acid

How to selectively deprotect the C4-OH

NaBH4

How to selectively deprotect the C6-OH

LiAlH4

Which coupling reagent should be used during SPPS and why?

DIC because DCC produces an insoluble urea byproduct

What do we generally use to protect the N-terminus for SPPS and why?

Fmoc, Boc uses acidic conditions to deprotect which would release the peptide from the resin.

What can we use to activate the anomeric hydroxyl group in glycosidic bond formation?

HBr (followed by Ag2CO3 and AgOTf), CCl3CN + NaH (activated by TMSOTf), PhSH + BF3 (followed by further activation)

What often leads to the major product of glycosidic bond formation being alpha?

anomeric effect

What effect leads to the formation of the 1,2-trans isomer in glycosidic bond formation?

neighbouring group participation, usually a ester protecting group

what is intramolecular tethering used for the formation of?

1,2-cis glycosidic bonds

What is commonly used for intramolecular tethering?

Me2SiCl2

How to selectively protect a primary OH of a sugar?

Triphenyl methyl ether (Trityl)