Nucleic Acids in Chemistry and Biology

intermediates do not require further protection at phosphorus and are rapidly and efficiently activated by a
range of condensing agents, such as pivaloyl chloride (Figure 3.53). This can be carried out before or after
the addition of the second nucleoside if excess condensing agent is avoided. A dinucleoside H-phosphonate
is rapidly formed in high yield. The procedure can be repeated many times before a single oxidation step
finally converts the H-phosphonate diesters into phosphate diesters (Figure 3.57). Studies on the mech-
anism of condensation indicate that a mixed phosphonate anhydride is the likely intermediate.

3.2.3.6 Synthesis of Phosphate Monoesters.34,90 Monoesters are usually made either from triesters

by selective deprotection or by direct condensation of an alcohol with a reactive phosphorylating agent,
usually a polyfunctional species such as phosphoryl chloride(POCl 3 ). The first formed product is imme-
diately hydrolysed to give the desired monoester.
Triester procedures almost always call for selective protection of the nucleoside hydroxyl groups to
leave only the reaction centre free. Reagents such as dibenzyl phosphorochloridate (with deprotection via
catalytic hydrogenolysis), bis-(2,2,2-trichloroethyl) phosphorochloridate (deprotection by zinc reduction)
or 1,2-phenylene phosphorochloridate (deprotection by hydrolysis to the diester and then oxidative removal
of catechol) give good yields of phosphate monoester (Figure 3.58a). Selective reaction at the 5-hydroxyl

110 Chapter 3

Me

Cl Me

3 C

Me

Me

Cl 3 C

O

P

O O

Cl

O

P

O O

Cl

HO O

R

B

HO

PO O

HO

B P

O P X

O

O

CN

O

HO R

Cl P O B

X

Cl

O

P

O O

OR

RCH 2 O

P(OCMe 2 CCl 3 ) 2

O

HO O

O

B

O PO

X

O P OR

O

O

O P OR

O

O

O

HO R

O P O B

O

X

B=Ade, Cyt, Gua, Thy, Ura or modified base X=O,S

R = OH, H, F

+ ROH

+ RCH 2 OH

a

b

c

P = protecting group

+

X=O,S

(i) (ii), (iii)

(i) (iv)

(v) (ii)

(vi), (vii)

Figure 3.58 Syntheses of phosphate monoesters. (a) Triester procedures, (b) using POCl 3 or PSCl 3 , (c) synthesis of
3 -phosphate monoesters. Reagents: (i) base; (ii) aq. Et 3 NHHCO 3 ; (iii) Br 2 /H 2 O (oxidation);
(iv) Zn, MeCO 2 H; (v) POCl 3 [PSCl 3 (collidine for pyrimidine nucleosides)] in (MeO) 3 PO, 0°C;
(vi) DCC, pyridine; and (vii) aq. NH 4 OH(XO) or tBuNH 2 /pyridine then aq. NH 4 OH(XS)

PCl 3 P

O

H

O

OR

P

H

R'O

O

OR

P

O

R'O

O

OR HO

HO

R= 3'

5'

(i) (ii) (iii) R' =

Figure 3.57 Synthesis of phosphate diesters via H-phosphonates. Reagents: (i) ROH then aq. Et 3 N; (ii) (CH 3 ) 3 COCl
and ROH; and (iii) I 2 in aq. Pyridine

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