Nucleic Acids in Chemistry and Biology

very good leaving groups, the difference between mono- and dianion reactivity is small, but for poor leaving
groups, the monoanion is by far the more reactive ionic form and accounts totally for the observed reaction even
at high pH. Similar phenomena have been analysed for spontaneous hydrolyses of acetyl phosphate, creatine
phosphate and ATP (loss of the -phosphate), all of which have good leaving groups on a terminal phosphate.

3.2.3 Synthesis of Phosphate Diesters and Monoesters

The most common approaches to dinucleoside phosphate ester synthesis use phosphorylation reactions in
which a 3-nucleotide component is converted into a reactive phosphorylating species by a condensing
agent. One of the major problems is that the more reactive condensing agents not only activate the phos-
phate, but may also react with nucleoside bases or the product, leading to unacceptable reduction in yield.
The ideal condensing agent should have a high rate of activation of the phosphate species and a negligible
rate of reaction with the alcohol component or N-protected bases.

3.2.3.1 Interrelationships of Esters of Phosphorus Oxyacids. The formal relationship between

phosphorus halides (XCl) and the mono-, di- and tri-alkyl esters of phosphorus oxyacids is shown
schematically (Figure 3.53). Actual reaction conditions have to be controlled carefully to avoid the for-
mation of by-products, especially of alkyl halides. Many of the interconversions shown are best accom-
plished using nitrogen ligands at phosphorus (X i-Pr 2 N or an azole).

Nucleosides and Nucleotides 107

PO

O

O

HO

R

OP O

O

OO

H

H

R

H

PO

O

O

O

R

H

O P

O

OOH

H

OP

O

OO

H

H

+ H 2 O - ROH

Figure 3.52 Hydrolysis of a phosphate monoester monoanion through an ‘exploded’ transition state

X

X P

X X

RO P

RO OR

RO P

RO

O

X

RO P

X

O

OR

RO P

RO

O

X

RO P

RO

O

X

X P

X

H 2 O

O

O

RO P

O

O

O

RO P

RO

hydrolysis

X

RO P

X

O

H

RO P

OH HO

RO P

HO

O

H

RO P

RO OH

RO P

RO

H 2 O H 2 O

trialkyl phosphite

(phosphite triester)

ROH, base

phosphorus (V)

chemistry

trialkyl phosphate

(phosphate triester)

ROH, base ROH, base

monoalkyl phosphate

(phosphate monoester)

ROH, DCC

dialkyl phosphate

(phosphate diester)

ROH,

MST or MSNT

oxidation t-BuOOH

(oxidation)

ROH, base ROH, base ROH, base

phosphorus (III)

chemistry

ROH, t-BuCOCl

H-phosphonate diester

oxidation oxidation

Figure 3.53 Formal relationship between exters of P(III) and P(V) oxyacids. DCC N,N-dicyclohexylcarbodiimide,
MSTmesitylenesulfonyl tetrazolide, MSNTmesitylenesulfonyl (3-nitrotriazolide)