Trimethylchlorosilane: A novel activating reagent in nucleotide synthesis via the phosphoramidite route

Article abstract of DOI:10.1039/a701924f

Trimethylchlorosilane (TMSCl) is a remarkably efficient activator in the reaction of phosphorus(III) amides with nucleosides to give phosphorus(III) esters in excellent yield.

Full text of DOI:10.1039/a701924f

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Trimethylchlorosilane: a novel activating reagent in nucleotide synthesis via
the phosphoramidite route
Wojciech Dabkowski,a Izabela Tworowska,a Jan Michalski*a and Friedrich Cramerb
a Centre of Molecular and Macromolecular Studies, Polish Academy of Science, 90-363 Lo´dz´, Sienkiewicza 112, Poland
b Max-Planck-Institut fu¨r experimentelle Medizin, 3400 Go¨ttingen, Hermann-Rein Strasse 3, Germany
Trimethylchlorosilane (TMSCl) is a remarkably efficient
activator in the reaction of phosphorus(III) amides with
nucleosides to give phosphorus(III) esters in excellent yield.
Excellent coupling procedures activated by TMSCl were
noted for PIII amides containing a fluorine ligand. For example,
fluoro(diisopropylamino)-2-cyanoethoxyphosphine 6§ reacts
with 5A-O-DMTr-nucleoside 4a,b in the presence of TMSCl
(0.6 equiv.) to give 5A-O-DMTr-thymidine 3A-O-(2-cyanoethyl)-
fluorophosphite 7a and N6-benzoyl-5A-O-DMTr-adenosine
3A-O-(2-cyanoethyl)fluorophosphite 7b¶ in almost quantitative
yield. The analogous reaction activated by tetrazole requires a
5-fold excess of activator and proceeds distinctly more
slowly.
Efficient synthesis of 5A-O-DMTr-thymidine (3A-5A) 3A-O-
DMT-thymidine phosphorfluoridite 10a and N6-benzoyl-5A-O-
DMT-2A-deoxyadenosine (3A-5A)-3A-O-DMTr-thymidine phos-
phofluoridite 10b∑ was achieved by coupling of
3A-O-nucleosidyl-phosphorfluoroamidites 88 with a 3A-O-pro-
tected nucleoside in the presence of TMSCl (0.3 equiv.). The
analogous reaction activated by tetrazole proceeds more slowly
and requires a large excess of the activator.9
Synthesis of the 5A-O-DMTr-thymidine difluorophosphine
12** was achieved by the coupling of diisopropylamino-
difluorophosphine 118 with 3A-O-protected nucleosides in the
presence of TMSCl activator.
The mechanism of activation by TMSCl is presumed to
involve its reaction with PIII amide. This type of interaction has
been discussed in our earlier paper5 and more recently by
Nifantyev.10 The first step produces salt-like species R2P+(Si-
Me3)NRB2Cl2 and R2PN+RB2(SiMe3)Cl2 which react either
Phosphoramidites are among the most important reagents in the
synthesis of phosphates of biological interest by the ‘phosphite
approach’.1 Tetrazole, tetrazole salts with amines and structural
analogues of this heterocycle are generally used as activators of
the reaction between alcohols and phosphoramidites.2 Tetra-
zole, the most widely employed activator, must often be used in
excess and be of high purity, which involves hazardous
sublimation. Other activators like amine hydrochlorides3 and
acyl chlorides that act via intermediate formation of phosphor-
chloridites4 have been used only occasionally.
In our recent studies on the synthesis of modified nuclotides
we were confronted with the challenge of finding an alternative
mode of activation without using tetrazole or similar com-
pounds. Our earlier work on interaction of PIII amides with
halogenosilanes5 suggested to us that phosphoramidites would
react with alcohols in the presence of trimethylchlorosilane
(TMSCl) as catalyst. This proved to be so, and was highly
efficacious from a preparative point of view. The reaction of PIII
amidites with an equivalent amount of nucleoside proceeds in
the presence of TMSCl in very high yield and at rates
comparable or higher than those when tetrazole is used.
Phosphitylations activated by TMSCl proceed at room tem-
perature in solvents like THF, CH2Cl2 or MeCN. On average,
the amount of activator required for an efficient coupling is ca.
30–60% of the stoichiometrical ratio. Most of our experiments
were performed with PIII amides derived from diisopropylamine
in order to conform to the most popular phosphitylation
procedures. Selected examples illustrating our metholology are
chosen from nucleotide chemistry.†
DMTrO
B
O
OH
4a B = Th
b B = Ad(Bz)
A remarkable example of activation in the presence of a
catalytic amount of TMSCl (0.6 equiv.) is the reaction of
thymidine 1 with tris(dimethylamino)phosphine to give thymi-
dine 3A,5A-cyclic dimethylphosphoramidite 2 in 95% yield.
Activation by tetrazole is less effective in this case.The yield of
cyclic amidite 2 is poor in the absence of TMSCl.6
DMTrO
B
O
N
Me3SiCl
POCH2CH2CN
+
HN
2
3
O
P
N
Commercially available bis(diisopropylamino)-2-cyano-
ethoxyphosphine reacts in the presence of TMSCl (0.6 equiv.)
with 5A-O-DMTr-nucleoside in a highly selective way to form
5A-O-DMTr-thymidine 3A-O-(2-cyano-N,N-diisopropyl)phos-
phoramidite 5a and N6-benzoyl-5A-O-DMTr-deoxyadenosine
3A-O-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite 5b‡ in
over 97% yield. In this case the yield and purity of amidites 5a,b
are identical to those obtained by activation with tetrazole.7
NCCH2CH2O
5a,b
Scheme 2 Reagents and conditions: 4 (1.0 equiv.), 3 (1.0 equiv.), TMSCl
(0.6 equiv.), THF, room temp., 1 h
OCH2CH2CN
DMTrO
B
O
N
P
F
6
4
Th
+
HN
HO
Th
O
Me3SiCl
O
O
P
F
P(NMe2)3
Me3SiCl
O
+ 2 HNMe2
NCCH2CH2O
P
O
7a B = Th
b B = Ad(Bz)
OH
Me2N
1
2
Scheme 1 Reagents and conditions: 1 (1.0 equiv.), P(NMe2)3 (1.0 equiv.),
Scheme 3 Reagents and conditions: 4 (1.0 equiv.), 6 (1.0 equiv.), TMSCl
TMSCl (0.6 equiv.), THF, room temp., 2 h
(0.6 equiv.), THF, room temp., 1 h
Chem. Commun., 1997
877

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81.014 MHz, H3PO4 external standard; 19F 188.15 MHz, CFCl3 external
standard). TMSCl was freshly distilled.
HO
B′
DMTrO
B
O
DMTrO
B
O
O
‡ Selected data for 5a: yield 97%; dP (CDCl3): 147.37, 147.93. For 5b yield
ODMTr
9
98%; dP (CDCl3): 147.49, 147.37.
§ Compound 6 was prepared in 90% yield from chloro(diisopropylamino)-
2-cyanoethoxyphosphine via 2-cyanoethoxy(diisopropyl)amino-4-nitro-
phenoxyphospine by standard ligand exchange procedures (ref. 8). dP
(CDCl3): 162.8, 148.9 (JP–F 111.8.1 Hz); dF (CDCl3): 275.1, 281.06
(JP–F 1118.4 Hz).
¶ Selected data for 7a: yield 97%; dP (C6D6): 138.02, 123.03, 137.78,
122.78; dF (C6D6): 253.07, 259.51 (JP–F 1214.07 Hz), 253.44, 259.90
(JP–F 1216.05 Hz). For 7b: yield 95%; dP (C6D6): 138.90 , 123.47; dF
(C6D6): 252.99, 259.46 (JP–F 1216.9 Hz), 253.19, 259.58 (JP–F 1216.8
Hz).
∑ Selected data for 10a: yield 98%; dP (CDCl3): 138.42, 123.35, 139.72,
124.61; d (CDCl3): 253.91, 260.21 (JP–F 1220.63 Hz), 253.61, 260.07
(JP–F 1224.03 Hz). For 10b: yield 98%, dP (CDCl3): 138.50, 123.47, 140.04,
124.90; dP (CDCl3): 252.18, 258.66 (JP–F 1221.24 Hz), 252.77, 259.29
(JP–F 1226.99 Hz).
O
O
N
P
O
B′
Me3SiCl
P
F
F
ODMTr
8
10a B = Th, B′ = Th
b B = Ad(Bz), B′ = Th
Scheme 4 Reagents and conditions: 8 (1.0 equiv.), 9 (1.0 equiv.), TMSCl
(0.30 equiv.), THF, room temp., 1 h
DMTrO
B
F
F
O
N
P
** Selected data for 12: yield 95%; dP (CDCl3): 128.58, 111.77,
95.79 (JP–F 1295.4, JP–F 1294.9 Hz); dF (CDCl3): 244.18, 251.06, 244.36,
251.63 (JP–F 1296.9, JP–F 1293.6 Hz).
11
Me3SiCl
HN
4
+
O
F
F
P
12
Scheme 5 Reagents and conditions: 4 (1.0 equiv.), 11 (1.1 equiv.), TMSCl
(0.6 equiv.), room temp., 1 h
References
1 R. L. Letsinger and W. B. Lunsford, J. Am. Chem. Soc., 1976, 98,
3655.
2 S. L. Beaucage and M. H. Caruthers, Tetrahedron Lett., 1981, 22, 1859;
E. Uhlman and A. Peyman, Chem. Rev., 1990, 90, 543; S. L. Beaucage
and R. P. Iyer, Tetrahedron, 1993, 48, 2223.
3 S. M. Gryaznov and R. L. Letsinger, Nucleic Acids Res., 1992, 20,
1879.
4 R. M. Karl, W. Richter, R. Klo¨sel, M. Mayer and I. Ugi, Nucleosides
Nucleotides, 1996, 15, 379.
5 M. Cypryk, J. Chojnowski and J. Michalski, Tetrahedron, 1985, 41,
2471.
6 G. Baschang and V. Kvita, Angew. Chem., 1973, 44; Angew. Chem., Int.
Ed. Engl., 1973, 12, 71; G. S. Bajwa and W. G. Bentrude, Tetrahedron
Lett., 1978, 5, 421.
7 A. Kraszewski and K. E. Norris, Nucleic Acids Res. Symp. Ser., 1987,
18, 177.
8 W. Dabkowski and I. Tworowska, Tetrahedron Lett., 1995, 36, 1095.
9 W. Dabkowski, I. Tworowska, J. Michalski and F. Cramer, J. Chem.
Soc., Chem. Commun., 1995, 1435.
directly with alcohol to give ester R2PORA or via intermediate
formation of R2PCl. In both cases TMSCl is regenerated. A
mechanistic path may be considered in which TMSCl reacts
with alcohol to form hydrogen chloride which then activates an
PIII amide in situ. But it is well known that TMSCl reacts very
slowly with alcohols unless a catalyst is present.11 Formation of
hydrogen chloride would effect the removal of the acid labile
DMTr group. This is actually observed when the commercial
TMSCl contaminated with HCl is used. However when
hydrogen chloride free TMSCl is utilized, this is not observed.
Work is currently in progress aimed at utilizing the TMSCl
activation for the synthesis of oligonucleotides on solids
supports and better understanding its mechanistic features.
This work was supported by the State Committee for
Scientific Research, Poland (No 3T09A 155 10), German–
Polish project (X084-9) and Perstorp Pharma, Perstop, Swe-
den.
10 M. K. Gratchev, V. Yu. Mishina and E. E. Nifantyev, Zh. Obshch.
Khim., 1993, 63, 1671.
11 J. G. Lee and K. K. Kang, J. Org. Chem., 1988, 53, 3634; D. C. Snyder,
J. Org. Chem., 1995, 60, 2638.
Footnotes
* E-mail: wdabkow@free.polbox.pl
† All manipulations were performed under argon and all solvents dried prior
to use. NMR spectra were recorded on a Bruker AC 200 spectrometer (31
Received in Glasgow, UK, 17th February 1997; Com.
7/01924F
P
878
Chem. Commun., 1997