Synthesis of Ribonucleosides by Condensation Using Trimethylsilyl Triflate

Helmut Vorbrüggen1, Irene M. Lagoja2, Piet Herdewijn2

1 Free University Berlin, Berlin, 2 Rega Institute for Medical Research, Leuven
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 1.13
DOI:  10.1002/0471142700.nc0113s27
Online Posting Date:  January, 2007
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Abstract

This unit describes, in detail, the optimized condition for the synthesis of nucleosides making use of the trimethysilyl triflate–mediated silyl‐Hilbert‐Johnson synthesis. This unit focuses on the mechanistic understanding of this universal and conveniently applicable method.

Keywords: nucleoside synthesis; glycosylation; Hilbert‐Johnson; Lewis acid catalysis; Vorbrüggen condensation

     
 
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Table of Contents

  • Basic Protocol 1: Preparation of Uridine
  • Basic Protocol 2: Preparation of Cytidine
  • Basic Protocol 3: Preparation of Adenosine
  • Basic Protocol 4: Preparation of Guanosine
  • Support Protocol 1: Preparation of Silylated Heterocycles Using HMDS
  • Support Protocol 2: Preparation of Silylated Heterocycles Using BSA
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Preparation of Uridine

  Materials
  • 2,4‐Bis(trimethylsilyloxy)pyrimidine (S.5; see protocol 5)
  • Anhydrous 1,2‐dichloroethane (reflux overnight on P 2O 5 and distill before use)
  • 1‐O‐Acetyl‐2,3,5‐tri‐O‐benzoylribofuranose (S.9)
  • Trimethylsilyltrifluoromethanesulfonate (TMSOTf; S.10)
  • Dichloromethane (CH 2Cl 2)
  • Methanol (MeOH)
  • Saturated sodium bicarbonate (sat. NaHCO 3) solution, ice cold
  • Sodium sulfate (Na 2SO 4)
  • Silica gel (0.060 to 0.200 nm)
  • Benzene (optional)
  • Saturated ammonia in methanol (sat. NH 3/MeOH)
  • Ethanol (EtOH)
  • 100‐ and 250‐mL round‐bottom flask
  • Balloon filled with nitrogen or argon
  • Reflux condenser
  • Precoated TLC plates (e.g., Alugram Sil G/UV 254, Macherey‐Nagel)
  • 254‐nm UV lamp (for TLC)
  • 500‐mL separatory funnel
  • 500‐mL Erlenmeyer flask
  • Buchner funnel
  • Filter paper
  • 250‐mL filter flask
  • Rotary evaporator equipped with a vacuum pump
  • 5 × 35–cm chromatography column
  • Desiccator
  • Additional reagents and equipment for TLC ( appendix 3D) and column chromatography ( appendix 3E)

Basic Protocol 2: Preparation of Cytidine

  Materials
  • 4‐(Trimethylsilylamino)‐2‐(trimethylsilyloxy)pyrimidine (S.6; protocol 5)
  • Anhydrous 1,2‐dichloroethane (reflux overnight over P 2O 5 and distill before use)
  • 1‐O‐Acetyl‐2,3,5‐tri‐O‐benzoylribofuranose (S.9)
  • Trimethylsilyltrifluoromethanesulfonate (TMSOTf, S.10)
  • Dichloromethane (CH 2Cl 2)
  • Methanol (MeOH)
  • Saturated sodium bicarbonate (sat. NaHCO 3) solution, ice cold
  • Sodium sulfate (Na 2SO 4)
  • Silica gel (0.060 to 0.200 nm)
  • Ethanol (EtOH), hot
  • Charcoal
  • Celite
  • Saturated ammonia in methanol (sat. NH 3/MeOH)
  • 250‐mL round‐bottom flask
  • Balloon filled with nitrogen or argon
  • Reflux condenser
  • Precoated TLC plates (e.g., Alugram Sil G/UV 254, Macherey‐Nagel)
  • 254‐nm UV lamp (for TLC)
  • 500‐mL separatory funnel
  • 500‐mL Erlenmeyer flask
  • Filter paper
  • Buchner funnel
  • 250‐mL filter flask
  • Rotary evaporator equipped with a vacuum pump
  • Desiccator
  • Additional reagents and equipment for TLC ( appendix 3D)

Basic Protocol 3: Preparation of Adenosine

  Materials
  • N6,9‐Bis(trimethylsilyl)‐N6‐benzoyladenine (S.7) obtained from 10 mmol N6‐benzoyladenine (see protocol 5)
  • 1‐O‐Acetyl‐2,3,5‐tri‐O‐benzoylribofuranose (S.9)
  • Anhydrous 1,2‐dichloroethane (reflux overnight on P 2O 5 and distill before use)
  • Trimethylsilyltrifluoromethanesulfonate (TMSOTf, S.10)
  • Dichloromethane (CH 2Cl 2)
  • Methanol (MeOH)
  • Saturated sodium bicarbonate (sat. NaHCO 3) solution, ice cold
  • Sodium sulfate (Na 2SO 4)
  • Silica gel (0.060 to 0.200 nm)
  • Petroleum ether (optional)
  • Saturated ammonia in methanol (sat. NH 3/MeOH)
  • 250‐mL round‐bottom flasks
  • Balloon filled with nitrogen or argon
  • Reflux condenser
  • Precoated TLC plates (e.g., Alugram Sil G/UV 254, Macherey‐Nagel)
  • 254‐nm UV lamp (for TLC)
  • 500‐mL separatory funnel
  • 500‐mL Erlenmeyer flask
  • Filter paper
  • Buchner funnel
  • 250‐mL filter flask
  • Rotary evaporator equipped with a vacuum pump
  • 5 × 50–cm chromatography column
  • Desiccator
  • Additional reagents and equipment for TLC ( appendix 3D) and column chromatography ( appendix 3E)

Basic Protocol 4: Preparation of Guanosine

  Materials
  • 6‐(Trimethylsilyloxy)‐2‐(N‐trimethylsilylacetamido)‐(N9‐trimethylsilyl)purine (S.8) obtained from 4.09 mmol N2‐acetylguanine (S.4) (see protocol 5)
  • 1‐O‐Acetyl‐2,3,5‐tri‐O‐benzoylribofuranose (S.9)
  • Anhydrous 1,2‐dichloroethane (reflux overnight on P 2O 5 and distill before use)
  • Trimethylsilyltrifluoromethanesulfonate (TMSOTf, S.10)
  • Dichloromethane (CH 2Cl 2)
  • Methanol (MeOH)
  • Saturated sodium bicarbonate solution (sat. NaHCO 3 solution), ice cold
  • Sodium sulfate (Na 2SO 4)
  • Silica gel (0.060 to 0.200 nm)
  • Saturated ammonia in methanol (sat. NH 3/MeOH)
  • 250‐mL round‐bottom flask
  • Balloon filled with nitrogen or argon
  • Reflux condenser
  • Precoated TLC plates (e.g., Alugram Sil G/UV 254, Macherey‐Nagel)
  • 254‐nm UV lamp (for TLC)
  • 500‐mL separatory funnel
  • 500‐mL Erlenmeyer flask
  • Filter paper
  • Buchner funnel
  • 250‐mL filter flask
  • Rotary evaporator equipped with a vacuum pump
  • 5 × 35–cm chromatography column
  • Desiccator
  • Additional reagents and equipment for TLC ( appendix 3D) and column chromatography ( appendix 3E)

Support Protocol 1: Preparation of Silylated Heterocycles Using HMDS

  Materials
  • Heterocyclic base, e.g., uracil (S.1), cytosine (S.2), N6‐benzoyladenine (S.3), or N2‐acetylguanine (S.4)
  • Hexamethyldisilazane (HMDS)
  • Ammonium chloride (NH 4Cl)
  • Trimethylchlorosilane (TCS)
  • Pyridine
  • Xylenes (mixture of isomers, extra pure; Acros)
  • 50‐mL round‐bottom flask
  • Reflux condenser

Support Protocol 2: Preparation of Silylated Heterocycles Using BSA

  Materials
  • Heterocyclic base, e.g., uracil (S.1), cytosine (S.2), N6‐benzoyladenine (S.3), or N2‐acetylguanine (S.4)
  • Anhydrous 1,2‐dichloroethane
  • Nitrogen source
  • N,O‐Bis(trimethylsilyl)acetamide (BSA)
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Figures

Videos

Literature Cited

Literature Cited
   Framski, G., Gdaniec, Z., Gdaniec, M., and Boryski, J. 2006. A reinvestigated mechanism of ribosylation of adenine under silylating conditions. Tetrahedron 62:10123‐10129.
   Garner, P. and Ramakanth, S. 1988. A region‐controlled synthesis of N7‐ and N9‐guanine nucleosides. J. Org. Chem. 53:1294‐1298.
   Niedballa, U. and Vorbrüggen, H. 1970. A general synthesis of pyrimidine nucleosides. Angew. Chem. Int. Ed. 9:461‐462.
   Niedballa, U. and Vorbrüggen, H. 1974a. Synthesis of nucleosides. 9. General synthesis of N‐glycosides. I. Synthesis of pyrimidine nucleosides. J. Org. Chem. 39:3654‐3659.
   Niedballa, U. and Vorbrüggen, H. 1974b. Synthesis of nucleosides. 10. General synthesis of N‐glycosides. II. Synthesis of 6‐methyluridines. J. Org. Chem. 39:3660‐3663.
   Niedballa, U. and Vorbrüggen, H. 1974c. Synthesis of nucleosides. 11. General synthesis of N‐glycosides. III. Simple synthesis of pyrimidine disaccharide nucleosides. J. Org. Chem. 39:3664‐3667.
   Niedballa, U. and Vorbrüggen, H. 1974d. Synthesis of nucleosides. 12. General synthesis of N‐glycosides. IV. Synthesis of nucleosides of hydroxy and mercapto nitrogen heterocycles. J. Org. Chem. 39:3668‐3671.
   Niedballa, U. and Vorbrüggen, H. 1974e. Synthesis of nucleosides. 13. General synthesis of N‐glycosides. V. Synthesis of 5‐azacytidines. J. Org. Chem. 39:3672‐3673.
   Niedballa, U. and Vorbrüggen, H. 1976. Synthesis of nucleosides. 17. A general synthesis of N‐glycosides. 6. On the mechanism of the stannic chloride catalyzed silyl Hilbert‐Johnson reaction. J. Org. Chem. 41:2084‐2086.
   Vorbrüggen, H. and Bennua, B. 1981. Nucleoside syntheses. XXV. A new simplified nucleoside synthesis. Chem. Ber. 114:1279‐1286.
   Vorbrüggen, H. and Hoefle, G. 1981. Nucleoside syntheses. XXIII. On the mechanism of nucleoside synthesis. Chem. Ber. 114:1256‐1268.
   Vorbrüggen, H. and Krolikiewicz, K. 1975. New catalysts for nucleoside synthesis. Angew. Chem. 87:417.
   Vorbrüggen, H. and Ruh‐Pohlenz, C. 2000. Synthesis of nucleosides. Organic Reactions 55:1‐630.
   Vorbrüggen, H. and Ruh‐Pohlenz, C. 2001. Handbook of Nucleoside Synthesis. Wiley Interscience, New York.
   Vorbrüggen, H., Niedballa, U., Krolikiewicz, K., Bennua, B., and Höfle, G. 1978. On the mechanism of nucleoside synthesis. In Chemistry and Biology of Nucleosides and Nucleotides (R.E. Harman, R.K. Robins, and L.B. Townsend, eds.) pp. 251‐266. Academic Press, New York.
   Vorbrüggen, H., Krolikiewicz, K., and Bennua, B. 1981. Nucleoside syntheses. XXII. Nucleoside synthesis with trimethylsilyl triflate and perchlorate as catalysts. Chem. Ber. 114:1234‐1255.
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