1,2-Ethylene-3,3-bis(4′,4′′-dimethoxytrityl Chloride) (E-DMT): Synthesis and Applications of a Novel Protecting Reagent

Abstract

1,2-Ethylene-3,3-bis(4′,4′′-dimethoxytrityl chloride), (E-DMT) was developed as a novel, bifunctional protecting reagent. This new compound was found to have a potential as a multipurpose acid-labile protecting reagent which can afford a 5′,5′-tritylthymidine dimer and a unique 5′,3′-cyclic protected thymidine derivative in modest to good yields.

bis(trityl chloride) - bifunctional protecting reagent - acid-labile protecting group - solution-phase DNA synthesis - nucleo­side - thymidine

References

<A NAME="RS00104ST-1">1</A> For a review, see: Greene TW. Wuts PGM. Protective Groups in Organic Synthesis   3rd Ed.:  Wiley; New York: 1999.  p.102-112  

<A NAME="RS00104ST-2A">2a</A> For a review, see: Seliger H. In Current Protocols in Nucleic Acid Chemistry   Beaucage SL. Bergstrom DE. Glick GD. Jones RA. Wiley; New York: 2000.  Chap. 2.3.1-2.3.34.

<A NAME="RS00104ST-2B">2b</A> Successful use of trityl groups as acid-labile 5′-protecting groups was originally reported by Khorana et al. in: Gilman PT. Khorana HG. J. Am. Chem. Soc.  1958,  80:  6212-6222  

<A NAME="RS00104ST-2C">2c</A> See also: Smith M. Rammler DH. Goldberg IH. Khorana HG. J. Am. Chem. Soc.  1962,  84:  430 

<A NAME="RS00104ST-3">3</A> Biernat J. Wolter A. Köster H. Tetrahedron Lett.  1983,  24:  751 

<A NAME="RS00104ST-4">4</A> For a review of the recent studies on bifunctional trityl chlorides, see: Shchepinov MS. Korshun VA. Chem. Soc. Rev.  2003,  32:  170 

<A NAME="RS00104ST-5A">5a</A> Bonora GM. Rossin R. Zaramella S. Cole DL. Eleuteri A. Ravikumar VT. Org. Proc. Res. Dev.  2000,  4:  225 

<A NAME="RS00104ST-5B">5b</A> Reese CB. Yan H. J. Chem. Soc., Perkin Trans. 1  2002,  2619 

<A NAME="RS00104ST-6">6</A> Sanghvi YS. Andrade M. Deshmukh RR. Holmberg L. Scozzari AN. Cole DL. In Manual of Antisense Methodology   Hartmann G. Endres S. Kluwer Academic Publishers; Norwell, MA: 1999.  p.3-23  

<A NAME="RS00104ST-7">7</A> Pon RT. Current Protocols in Nucleic Acid Chemistry   Beaucage SL. Bergstrom DE. Glick GD. Jones RA. Wiley; New York: 2000.  Chap. 3.1.1-3.1.28. and references therein

<A NAME="RS00104ST-8">8</A> Mihaichuk JC. Hurley TB. Vagle KE. Smith RS. Yegge JA. Pratt GM. Tompkins CJ. Sebesta DP. Pieken WA. Org. Proc. Res. Dev.  2000,  4:  214 

<A NAME="RS00104ST-9A">9a</A> Ravikumar VT. Wyrzykiewicz TK. Cole DL. Tetrahedron  1994,  50:  9255 

<A NAME="RS00104ST-9B">9b</A> Krotz AH. Cole DL. Ravikumar VT. Tetrahedron Lett.  1996,  37:  1999 

<A NAME="RS00104ST-9C">9c</A> Ravikumar VT. Cheruvallath ZS. Cole DL. Nucleosides Nucleotides  1997,  16:  1709 

<A NAME="RS00104ST-9D">9d</A> Bhat B. Sanghvi YS. Tetrahedron Lett.  1997,  38:  8811 

<A NAME="RS00104ST-10A">10a</A> Krotz AH. Carty RL. Scozzari AN. Cole DL. Ravikumar VT. Org. Proc. Res. Dev.  2000,  4:  190 

<A NAME="RS00104ST-10B">10b</A> Pon RT. Yu S. Guo Z. Deshmukh R. Sanghvi YS. J. Chem. Soc., Perkin Trans. 1  2001,  2638 

<A NAME="RS00104ST-10C">10c</A> Sanghvi YS. Guo Z. Pfundheller HM. Converso A. Org. Proc. Res. Dev.  2000,  4:  175 

<A NAME="RS00104ST-11A">11a</A> Wen K. Chow S. Sanghvi YS. Theodorakis EA. J. Org. Chem.  2002,  67:  7887 

<A NAME="RS00104ST-11B">11b</A> Chow S. Wen K. Sanghvi YS. Theodorakis EA. Bioorg. Med. Chem. Lett.  2003,  13:  1631 

<A NAME="RS00104ST-12">12</A> Ramage R. Wahl FO. Tetrahedron Lett.  1993,  34:  7133 

<A NAME="RS00104ST-13">13</A> Goswami S. Mahapatra AK. Tetrahedron Lett.  1998,  39:  1981 

<A NAME="RS00104ST-14">14</A> Windisch B. Vögtle F. Nieger M. Lahtinen T. Rissanen K. J. Prakt. Chem.  2000,  342:  642 

<A NAME="RS00104ST-15">15</A>

Compound 3b was purchased from TCI (www.tciamerica.com).

<A NAME="RS00104ST-16">16</A>

The purity of the complex can roughly be checked by the color of the complex and/or the solution of it since the green color of Co(I)Cl(PPh₃)₃ is changed into blue color of Co(II) species generated by degradation.

<A NAME="RS00104ST-17">17</A> Wakatsuki Y. Yamazaki H. Inorg. Synth.  1989,  26:  189 

<A NAME="RS00104ST-18">18</A>

Experimental for Synthesis of 2: Ethyl ester 4a (1.96 g, 6.0 mmol) was dried by repeated coevaporations with dry toluene and dissolved in dry THF (30 mL) under argon. Freshly prepared 1 M p-anisyl magnesium bromide solution in dry THF was added drop wise to the mixture under reflux and stirred for 30 min. The mixture was cooled to r.t., diluted with Et₂O (150 mL), and washed with sat. NH₄Cl aq solution (150 mL). The aqueous layer was back-extracted with Et₂O (2 × 150 mL). The combined organic layers were washed with sat. NaCl aq solution (150 mL), dried over MgSO₄, filtered, and concentrated to dryness. The residue was dried by repeated coevaporations with dry toluene and dissolved in AcCl (3 mL). The mixture was heated under reflux for 1.5 h, and then cooled to r.t. The mixture was added to cyclohexane (30 mL), stirred for 5 min, and kept at 4 °C for 20 h. The mixture was warmed to r.t. and the resultant precipitate was collected by suction filtration. The collected solid was washed with dry cyclohexane (5 × 3 mL) and dried under vacuum to afford 2 (2.97 g, 4.22 mmol, 70%) as an orange powder. ¹H NMR (400 MHz, CDCl₃): δ = 7.16-7.11 (m, 4 H), 7.08 (d, J = 8.8 Hz, 8 H), 7.01 (d, J = 7.6 Hz, 2 H), 6.94 (d, J = 8.8 Hz, 2 H), 6.78 (d, J = 8.8 Hz, 8 H), 3.80 (s, 12 H), 2.86 (s, 4 H). ¹³C NMR (100 MHz, CDCl₃): δ = 158.7, 145.4, 140.6, 137.6, 130.9, 129.9, 127.9, 127.3, 127.1, 112.8, 82.5, 55.3, 37.5. ESI-MS: m/z for C₄₄H₄₁Cl₂O₄ (M + H⁺) 703. Anal. Calcd. for C₄₄H₄₀Cl₂O₄: C, 75.10; H, 5.73; Cl, 10.08. Found: C, 74.68; H, 6.07; Cl, 9.51.

<A NAME="RS00104ST-19">19</A>

Analytical data for 7: ¹H NMR (400 MHz, DMSO-d ₆): δ = 11.3 (brs, 2 H), 7.50 (s, 2 H), 7.19-7.14 (m, 14 H), 6.94-6.93 (m, 2 H), 6.85-6.82 (m, 8 H), 6.20 (dd, J = 6.7, 6.7 Hz, 2 H), 5.32 (d, J = 4.4 Hz, 2 H), 4.33 (m, 2 H), 3.84 (m, 2 H), 3.71 (s, 12 H), 3.12 (m, 4 H), 2.72 (s, 4 H), 2.24 (ddd, J = 13.5, 6.7, 6.7 Hz, 2 H), 2.15 (ddd, J = 13.5, 6.7, 3.2 Hz, 2 H), 1.38 (s, 6 H). ¹³C NMR (100 MHz, DMSO-d ₆): δ = 163.4, 157.8, 157.8, 150.1, 143.8, 140.4, 135.6, 135.4, 135.2, 129.5, 129.3, 127.8, 127.6, 126.7, 125.3, 113.0, 109.4, 85.7, 85.4, 83.6, 79.1, 70.5, 63.6, 55.0, 37.1, 11.7. HRMS: calcd for C₆₄H₆₅N₄Na₂O₁₄ ⁺ (M - H⁺ +2 Na⁺) 1159.4287; found: 1159.4342.

<A NAME="RS00104ST-20">20</A>

Analytical data for 8: ¹H NMR (400 MHz, CDCl₃): δ = 8.04 (brs, 1 H), 7.54 (s, 1 H), 7.37-6.69 (m, 24 H), 6.56 (dd, J = 9.2, 5.2 Hz, 1 H), 4.34 (m, 1 H), 4.04 (m, 1 H), 3.80 (s, 3 H), 3.78 (s, 3 H), 3.76 (s, 3 H), 3.72 (s, 3 H), 3.15-2.57 (m, 6 H), 2.27 (dd, J = 10.8, 3.2 Hz, 1 H), 2.11 (m, 1 H), 1.41 (s, 3 H). ¹³C NMR (100 MHz, CDCl₃): δ = 163.3, 158.6, 158.2, 158.1, 157.8, 150.0, 141.6, 141.5, 140.5, 140.1, 139.8, 138.5, 136.9, 135.6, 133.9, 130.9, 130.8, 129.4, 129.3, 129.3, 128.2, 127.7, 127.7, 127.6, 127.4, 127.3, 127.1, 113.2, 113.1, 113.0, 112.9, 110.8, 87.6, 86.6, 86.2, 85.5, 75.5, 55.3, 55.3, 55.3, 55.2, 40.4, 37.6, 36.8, 11.8. HRMS: calcd for C₅₄H₅₃N₂O₉ (M + H⁺) 873.3745; found: 873.3732.

<A NAME="RS00104ST-21A">21a</A> Furusawa K. Katsura T. Tetrahedron Lett.  1985,  26:  887 

<A NAME="RS00104ST-21B">21b</A> Beijer B. Grøtli M. Douglas ME. Sproat BS. Nucleosides Nucleotides  1994,  13:  1905 

<A NAME="RS00104ST-21C">21c</A> Wada T. Tobe M. Nagayama T. Furusawa K. Sekine M. Tetrahedron Lett.  1995,  36:  1683 

<A NAME="RS00104ST-22">22</A>

E-DMT is commercially available from Sai Dru Syn Laboratories, Hyderabad, India (www.saiintgroup.com).