Chemoselective Deprotection of Triethylsilyl Ethers

Abstract

An efficient and selective method was developed for the deprotection of triethylsilyl (TES) ethers using formic acid in methanol (5–10%) or in methylene chloride 2–5%) with excellent yields. TES ethers are selectively deprotected to the corresponding alcohols in high yields using formic acid in methanol under mild reaction conditions. Other hydroxyl protecting groups like t-butyldimethylsilyl (TBDMS) remain unaffected.

INTRODUCTION

Selective and efficient protection and deprotection plays a central role in the completion of multistep syntheses of organic molecules. For example, trityl,[1] triethylsilyl,[2] and tert-butyldimethylsilyl[3] ethers are normally used for selective protection of primary/secondary alcohols, particularly in carbohydrate and nucleoside/nucleotide chemistry. However, despite the ubiquity of these protecting groups in organic synthesis, only a few methods exist for selectively deprotecting them.[4] The selective deprotection of triethylsilyl (TES) ethers in the presence of tert-butyldimethylsilyl (TBDMS) can be carried out using 10% Pd/C in methanol or 95% ethanol,[5] mesoporous silica MCM-41/MeOH,[6] IBX in dimethyl sulfoxide (DMSO),[7] and 1-chloroethyl chloroformate in methanol.[8] These methods work well in many cases, however all require expensive reagents or catalysts. Our interest in synthesizing 5,6-dihydro-5-(α-thyminyl)-thymine has led us to develop a new method for the chemoselective deprotection of triethylsilyl ethers that is both efficient and economical.

5,6-Dihydro-5-(α-thyminyl)-thymine, or spore photoproduct (SP), is a methylene-bridged thymine dimer formed in spore DNA on ultraviolet (UV) irradiation (Scheme 1).[9,10] Scheme 1 first mention SP is the primary DNA photoproduct of UV irradiation of bacterial spores, and the extreme UV resistance of bacterial spores is due in part to the efficient repair of SP on spore germination. The repair of SP is catalyzed by the enzyme spore photoproduct lyase (SPL), which utilizes an iron-sulfur cluster and S-adenosylmethionine (AdoMet) to generate a putative 5′-deoxyadenosyl radical intermediate, which abstracts a hydrogen atom from C-6 of SP to initiate a radical-mediated β-scission.[11–14] Developing an understanding of the DNA repair mechanism of SPL has been hindered due to the unavailability of the pure spore photoproduct; in fact, most enzymatic studies in the literature involve the use of UV-irradiated DNA—an inherently impure substance containing numerous different types of damage—as a substrate. Currently, only limited synthetic routes are available in the literature for the generation of pure spore photoproduct with a phosphodiester linkage.[15] Our ongoing efforts to understand the SPL mechanism have led us to develop efficient methods for the synthesis of SP.

SCHEME 1.

Formation and Repair of SP.

RESULTS AND DISCUSSION

We report here an efficient and cost effective method for making the 5R and 5S-diastereomers of SP in high yields (Scheme 2) Scheme 2 first mention and their subsequent deprotection under mild reaction conditions (Scheme 3). Scheme 3 first mention The protected 5R and 5S-diastereomers (3 and 4) were prepared by coupling N³-trimethylsilylethoxymethyl-3, 5-di-triethylsilyl-5,6-dihydrothymidine 1 and 2-bromomethyl uridine 2 using LDA as a condensing reagent[15] at −78°C, which afforded 5R and 5S-diastereomers in a 3:4 ratio (Scheme 2). The 5R and 5S-diastereomers were easily purified on a silica gel column using a gradient of ethyl acetate and hexanes. The structures of these two closely related compounds were assigned on the basis of ¹H and ¹³C NMR (Table 1) Table 1 first mention as well as mass spectrometry, and the stereochemical assignments were made on the basis of two-dimensional nuclear Overhauser enhancement spectroscopy (NOESY) and rotational nuclear Overhauser effect spectroscopy (ROESY) data.[16] The C-5 methyl carbon of the 5R isomer (3) was observed at 22.03 ppm, whereas the methyl carbon of the 5S- isomer (4) was shifted 1.3 ppm to higher field at 20.73 ppm. However, only 0.04 ppm difference was observed in ¹H NMR of the 5R and 5S-isomers for the C-5 methyl group (Table 1). Differences in ¹H (at C-6 and the methylene bridge) and ¹³C (at C-5, C-6, and the methylene bridge) chemical shifts for the 5R and 5S isomers were also observed (Table 1).

SCHEME 2.

Formation of 5R and 5S-diastereomers.

SCHEME 3.

Selective deprotection of triethylsilyl ether using formic acid:methanol/methylene chloride.

TABLE 1.

¹H and ¹³C NMR of 3 and 4

Compound	Me	CH2 (base) C-6	CH2 (bridge)	C-5
3, 1H	1.18	3.03/3.15	2.60/2.68	-
3, 13C	22.03	44.25	32.34	42.91
4, 1H	1.14	3.0/3.27	2.49/2.75	-
4, 13C	20.73	44.90	32.29	42.24

The synthesis of SP from 3 and 4 involves the formation of a phosphodiester linkage between the sugar groups; this requires the selective deprotection of the 3′ and 5′-hydroxyls of 3 and 4. In this case, TES ethers must be deprotected selectively in the presence of TBDMS ethers. We have developed an efficient method for the deprotection of TES ethers in the presence of TBDMS ethers using 5–10% formic acid. Formic acid has been extensively used in carbohydrate chemistry/nucleoside chemistry as a deprotecting agent for trityl[17a] and isopropylidene[17b–d] groups, but so far no selective deprotection has been reported for TES versus TBDMS groups using formic acid. The 5R and 5S-protected thymidine dinucleosides 3 and 4 were prepared and separated in high yields as described above. Reaction of the protected dinucleosides of thymidine (3 and 4) separately with 5–10% formic acid:methanol at ambient temperature (Scheme 3), afforded 3′,5′-TES deprotected dinucleosides 5 and 6 in 70–85% yields. The 3′ and 5′ TBDMS groups of the dinucleosides remain unaffected under these reaction conditions (Table 2). Table 2 first mention The crude reaction mixture after workup showed only the desired product without any undesired side products. Reaction progress was conveniently monitored via thin-layer chromatography (TLC) and ¹H NMR, and the deprotection was generally complete within 2–3 hours.

TABLE 2.

Deprotection of compounds 3 and 4 using formic acid

Compound	Time (hours)	Conditions	Compound		Total yields (%)
			5	6
3	2	a	75	—	75
3	1	b	70	—	70
4	2	a	—	80	80
4	1	b	—	85	85
3	20–24	c	50–60	—	50–60
4	20–24	c	—	50–55	50–55

^a5% Formic acid:methanol (commercial ACS grade).

^b10% formic acid:methanol.

^c5% formic acid:CH₂Cl₂.

The deprotection of TES ethers generally proceeded more quickly in protic solvents than in nonprotic solvents. The deprotection reactions in methylene chloride were sluggish, with complete deprotection of TES ethers taking 20–24 hours (Table 2), consequently resulting in lower yields of the desired dinucleosides (50–60%). Under higher concentration of the formic acid in methanol (up to 20%), no deglycosylation or decomposition of the desired product was observed.

Triethylsilyl ethers can be easily deprotected in the presence of tert-butyldimethylsilyl ethers using 2% HF in acetonitrile or pyridine.[18] Deprotection of TES ethers of the thymidine dinucleosides 3 and 4 with 2–4% HF-pyridine resulted in only ~20–50% of the desired dinucleosides 5 and 6, along with primary (7, 9) and secondary (8, 10) TBDMS deprotected side products (Scheme 4). Scheme 4 first mention The structures of 5, 6, and the side products were easily deduced using one- and two-dimensional NMR methods. Higher concentrations of HF:pyridine and longer reaction times produce completely TBDMS/TES-desilylated products. Ultimately, the HF-pyridine method resulted in low yields of the desired thymidine dinucleoside for further synthesis of spore photoproduct.

Scheme 4.

Deprotection 5R & 5S-diastereomers (3 and 4) using 4% HF: pyridine.

The formic acid:methanol combination also works well for the selective deprotection of mononucleosides. 3′-O-tert-Butyldimethylsilyl-5′-O-triethylsilylthymidine 13 and 3′-O-tert-butyldimethylsilyl-5′-O-triethylsilyl-adenosine 17 were selectively deprotected in 70–76% yields using 5% formic acid:methanol (Scheme 5). Scheme 5 first mention Compound 13 was prepared from thymidine 11 in two steps. In first step, thymidine was selectively protected using 0.9 equivalents of triethylsilyl chloride in 95% yields followed by protection at the 3′ hydroxyl with tert-butyldimethylsilyl chloride. Compound 17 was also prepared similarly as described for 13. Deprotection using formic acid in methanol afforded compounds 14 and 18 in excellent yields (Scheme 5).

SCHEME 5. Selective deprotection of protected thymidine and adenosine.

Reagents and Conditions:

(i) TESCl, DMF, Imidazole, 95% (ii) TBDMSCl, DMF, Imidazole, rt., 93% (iii) MeOH:Formic acid, rt, 72–76%.

As control reactions, the 3′ and 5′ TBDMS-protected thymidine 19, the fully protected thymidine 20 (N³-Trimethylsilylethoxymethyl-3′, 5′-di-t-butyldimethylsilyl thymidine), and the 3′ and 5′ TES-protected dihydrothymidine 21 were stirred in 5–10% formic acid in methanol for 3–5 hours. NMR spectra of the reaction mixtures for 19 and 20 reveals that the TBDMS groups remain intact (Scheme 6). Scheme 6 first mention Even at higher concentrations of formic acid:methanol and over longer reaction periods, no deprotection of TBDMS was observed. In contrast, the TES-protected dihydrothymidine 3′, 5′-O-di-triethylsilyl-5, 6-dihydrothymidine (21), is deprotected in high yields under the same reaction conditions (Scheme 6).

SCHEME 6.

Deprotection of protected thymidine/5,6-dihydrothymidine.

EXPERIMENTAL

All reactions were carried out in oven- or flame-dried glassware under a nitrogen atmosphere. Solvents were distilled prior to use. Dichloromethane and pyridine were distilled from calcium hydride. Tetrahydronfuran (THF) was distilled on sodium/benzophenone prior to use. Purification of reaction products was carried out by flash chromatography using silica gel (230–400 mesh). All reagents were commercially available and used without further purification. All reactions were monitored by TLC using silica gel 60, F-254. Column chromatography was conducted using flash silica gel. ¹H NMR and ¹³C NMR spectra were recorded on Bruker DPX-300, Bruker DRX-500, or on Bruker DRX-600 (Bruker, Billerica, MA, USA). NMR spectra were recorded on solutions in deuterated chloroform (CDCl₃), with residual chloroform (δ 7.27 ppm for ¹H NMR and δ 77.0 ppm for ¹³C NMR) or deuterated methyl sulfoxide (DMSO-d6), with residual methyl sulfoxide (δ 2.50 ppm for ¹H NMR and δ 35.0 ppm for ¹³C NMR) taken as the standard, and were reported in parts per million (ppm). Abbreviations for signal coupling are as follows: s, singlet; d, doublet; t, triplet; q, quartet; m, multiplet. The multiplicities of the ¹³C NMR signals were determined by HMQC and DEPT techniques. Mass spectra (high resolution FAB or ESI) were recorded on a Q-Tof and 70-VSEs spectrometer at Noyes Laboratory, University of Illinois Urbana-Champaign.

General Procedures

Formic acid:Methanol Procedure for the Deprotection of TES Ethers

A solution of protected thymidine dinucleoside 3 or 4 (0.700 g, 0.58 mmol) in methanol (10 mL) was stirred at 5–10°C for 5 minutes followed by dropwise addition of a solution of 10% formic acid in methanol (10 mL). After complete addition of the formic acid solution, the cooling bath was removed and the reaction mixture was vigorously stirred for 1–2 hours at room temperature; TLC (ethyl acetate:hexanes 1:1) was used to monitor the progress of the reaction. Upon complete desilylation of TES groups to produce the dihydroxy dinucleoside, the reaction mixture was neutralized with 10% sodium bicarbonate solution (~20 mL) and the solvent was removed on a rotary evaporator under reduced pressure. The residue was dissolved in methylene chloride and washed with saturated sodium bicarbonate solution. The methylene chloride layer was dried over anhydrous sodium sulfate, concentrated, and the residue was purified on a silica gel column (flash chromatography) using a mixture of ethyl acetate:hexanes (50:50), resulting in the desired product as a white fluffy solid with 75–85% yield.

HF:Pyridine Procedure for the Deprotection of TES Ethers

A cold solution of 4% HF:pyridine (10 mL) was slowly added to a mixture of 5R or 5S-dinucleoside 3 or 4 (0.50 g, 0.41 mmol) in pyridine (5 mL) at 0–5°C while stirring. The reaction mixture was stirred at ambient temperature for 1–2 hours. The reaction progress was monitored using TLC. After completion of the reaction, the solution was cooled and the reaction mixture was neutralized with saturated sodium bicarbonate solution. The reaction mixture was concentrated under reduced pressure and the residue was dissolved in a mixture of methylene chloride and water (1:1, 100 mL). The organic layer was thoroughly washed with saturated sodium bicarbonate solution and dried over anhydrous sodium sulfate; finally, the solvent was removed under reduced pressure. The respective residues were loaded onto a silica gel column and the column was eluted with a 10–50% ethyl acetate:hexanes gradient to afford the desired dinucleosides.

Compound 3

Yield: 30%; viscous oil; R_f. 0.6; ¹H NMR (CDCl₃): δ −0.05 (s, 9H, CH₃), −0.03 (s, 9H, 3CH₃), 0.06 (s, 3H, CH₃), 0.07 (s, 3H, CH₃), 0.08 (s, 3H, CH₃), 0.086 (s, 3H, CH₃), 0.5–0.64 (m, 12H, CH₂), 0.87 (s, 9H, CH₃), 0.89 (s, 9H, CH₃), 0.89–0.91 (m, 22 H, 6CH₃ TES & CH₂ SEM), 1.18 (s, 3H, Me), 1.88–1.96 (m, 3H, CH₂, 2′), 2.18–2.2 (m, 1H, CH_, 2′), 2.60 (d, J = 14 Hz, 1H, CH₂, bridge), 2.6 (d, J = 14 Hz, 1H, CH₂, bridge), 3.03 (d, J = 13.5 Hz, 1H, CH₂, base), 3.15 (d, J = 13.5 Hz, 1H, CH₂, base), 3.52 (t, 2H, CH₂, SEM), 3.56 (dd, 2H, CH₂, 5′), 3.61 (dd, J = 8 Hz, 2H, CH₂, SEM), 3.7 (dd, J = 5.5 Hz, 2H, CH₂, 5′), 3.7–3.79 (m, 1H, CH, 4′), 3.8 (m, 1H, 4′), 4.2–4.2 (m, 1H, 3′), 4.4 (m, 1H, 3′), 5.1 (s, 2H, NCH₂, SEM), 5.3 (s, 2H, NCH₂, SEM), 6.2–6.3 (m, 2H, 1′), 7.4 (s, 1H, base); ¹³C NMR (CDCl₃): δ −5.4 (CH₃), −5.3 (CH₃), −4.8 (CH₃), −4.6 (CH₃), −1.4 (CH₃), −1.4 (CH₃), 4.2 (CH₂), 4.6 (CH₂), 6.7 (CH₃), 6.77 (CH₃), 17.9 (Cquat), 18.1 (CH₂), 18.3 (Cquat), 22.0 (CH₃ C5), 25.7 (Me, TBDMS), 25.9 (Me, TBDMS), 32.3 (CH₂ bridge), 36.8 (CH₂), 40.2 (CH₂), 42.9, 44.2 (CH₂-base), 62.8 (CH₂), 63.0 (CH₂), 66.6 (CH₂), 67.4 (CH₂), 69.9 (CH_2, SEM), 70.3 (CH_2, SEM), 71.9 (C 3′), 72.0 (C 3′), 84.3 (C 4′), 85.3 (C, 1′), 86.2 (C 1′), 87.4 (C 4′), 108.5 (Cquat), 139.1 (CH), 150.6 (Cquat), 152.2 (Cquat), 163.4 (Cquat), 173.6 (Cquat); HRMS: m/z: 1201.7001 (calcd. for C₅₆H₁₁₃N₄O₁₂Si₆; 1201.6971) (M + H); MS: (TOF, MS, ESI) m/z 1223, 1203, 1202, 1201, 1200, 1173, 1087, 859, 858, 857, 829, 801, 629, 628, 599.

Compound 4

Yield: 40%; viscous oil; R_f. 0.5; ¹H NMR (CDCl₃): δ −0.48 (s, 9H, CH₃), − 0.03 (s, 9H, 3CH₃), 0.056 (s, 3H, CH₃), 0.06 (s, 3H, CH₃), 0.07 (s, 6H, 2CH₃), 0.5–0.6 (m, 12H, CH₂), 0.8 (s, 9H, CH₃, TBDMS), 0.87 (s, 9H, CH₃ TBDMS), 0.9–0.9 (m, 4 H, 2 CH₂), 0.9 (s, 9H, TES), 0.9 (s, 9H, TES), 1.1 (s, 3H, Me), 1.9–2.01 (m, 3H, CH₂, 2′), 2.2 (dd, J = 7.5 Hz, 1H, CH_, 2′), 2.4 (d, J = 14 Hz, 1H, CH₂, bridge), 2.7 (d, J = 14 Hz, 1H, CH₂, bridge), 3.0 (d, J = 13.5 Hz, 1H, CH₂, base), 3.2 (d, J = 13.5 Hz, 1H, CH₂, base), 3.5 (t, J = 8 Hz, 2H, CH₂, SEM), 3.5 (dd, 2H, CH₂, 5′), 3.6 (t, J = 8.5 Hz, 2H, CH₂), 3.7 (dd, 2H, CH₂, 5′), 3.8 (bt, 1H, 4′), 3.91 (bt 1H, 4′), 4.2 (bt, 1H, 3′), 4.3 (bt, 1H, 3′), 5.1 (d, J = 9.5 Hz, 1H, CH₂, SEM), 5.1 (d, 1H, CH₂, SEM), 5.3 (s, 2H, CH₂, SEM), 6.2 (t, J = 6 Hz, 1H, 1′), 6.3 (t, 1H, 1′), 7.4 (s, 1H, base); ¹³C NMR (CDCl₃): δ −5.4 (CH₃), − 5.3 (CH₃), −4.8 (CH₃), −4.69 (CH₃), −1.4 (CH₃), 4.2 (CH₂), 4.6 (CH₂), 6.7 (CH₃), 6.7 (CH₃), 17.9 (Cquat), 18.0, 18.1, 18.3, 20.7 (CH₃), 25.7 (Me), 25.8 (Me), 32.2 (CH₂), 37.0 (CH₂), 40.7 (CH₂), 42.2 (Cquat), 44.9 (CH₂-base), 63.2 (CH₂), 63.3 (CH₂), 66.6 (CH₂), 67.3 (CH₂), 69.9 (CH₂), 70.0 (CH₂), 70.2, 72.1, 72.6, 72.73, 84.95, 86.22, 86.72, 87.97, 108.44 (Cquat), 137.9 (CH), 150.5 (Cquat), 152.5 (Cquat), 163.3 (Cquat), 173.5 (Cquat); HRMS: m/z: 1201.7021 (calcd. for C₅₆H₁₁₃N₄O₁₂Si₆; 1201.6971) (M + H); MS: (TOF, MS, ESI) m/z 1223, 1203, 1202, 1201, 1200, 1173, 1087, 859, 858, 857, 829, 801, 629, 628, 599.

Compound 5

Yield: 75%; R_f. 0.4; white fluffy solid; ¹H NMR (CDCl₃): δ −0.011 (s, 9H, CH₃, SEM), −0.01 (s, 9H, 3CH₃, SEM), 0.09 (s, 6H, CH₃, TBDMS), 0.1 (s, 6H, CH₃), 0.8 (s, 9H, CH₃), 0.8 (s, 9H, CH₃), 0.9–0.9 (m, 4H, 2CH₂), 1.1 (s, 3H, Me), 1.9–2.0 (m, 1H, CH₂, 2′), 2.0–2.1 (m, 1H, CH_, 2′), 2.2–2.27 (m, 2H, CH_, 2′), 2.33 (m, 1H, OH), 2.72–2.81 (m, 2H, CH₂, bridge), 3.09 (bt, 1H, OH), 3.19 (d, J = 13 Hz, 1H, CH₂, base), 3.51 (d, J = 13 Hz, 1H, CH₂, base), 3.58 (t, J = 8.5 Hz, 4H, CH₂, SEM), 3.68–3.78 (m, 4H, 5′), 3.8 (q, 1H, 4′) 3.9 (q, 1H, 4′), 4.41 (m, 1H, 3′), 4.4 (m, 1H, 3′), 5.1 (d, J = 9.5 Hz, 1H, CH₂, SEM), 5.2–5.2 (m, 2H, CH₂, SEM), 5.4 (d, 1H, CH₂, SEM), 6.2 (t, J = 7 Hz, 1H, 1′), 6.3 (t, J = 6 Hz, 1H, 1′), 7.5 (s, 1H, base); ¹³C NMR (CDCl₃): δ −5.4 (CH₃), −5.3 (CH₃), −4.8 (CH₃), −4.7 (CH₃), −1.5 (CH₃), −1.4 (CH₃), 17.87 (Cquat), 17.9 (CH₂), 18.1 (CH₂), 18.3 (Cquat), 20.8 (CH₃), 25.65 (Me), 25.8 (Me), 31.8 (CH₂), 37.4 (CH₂), 40.6 (CH₂), 42.1 (Cquat), 44.9 (CH₂-base), 62.4 (CH₂), 63.0 (CH₂), 66.6 (CH₂), 67.7 (CH₂), 69.8 (CH₂), 70.1 (CH₂), 72.1 (CH), 72.2 (CH), 85.5 (CH), 85.6 (CH), 86.1 (CH), 87.8 (CH), 108.5 (Cquat), 139.0 (CH), 150.5 (Cquat), 152.2 (Cquat), 163.5 (Cquat), 174.2 (Cquat); HRMS: m/z: 973.5267 (calcd. for C₄₄H₈₅N₄O₁₂Si₄; 973.5241) (M + H); MS: (TOF, MS, ESI) m/z 995 [M + Na], 973, 947, 946, 945, 917, 829, 801, 729; Anal. Calcd. for C₄₄H₈₄N₄O₁₂Si₄: C, 54.29; H, 8.70; N, 5.76; Found: C, 54.19, H, 8.74, N, 5.67.

Compound 6

The 5S-di-TBDMS dinucleoside was prepared in a similar manner as described for compound (5). Purification was carried out using a mixture of ethyl acetate:hexanes (50:50%) as eluent. Yield: 80%; R_f. 0.2; white fluffy solid; ¹H NMR (CDCl₃): δ −0.01 (s, 9H, 3CH₃ SEM), −0.02 (s, 3CH₃, 9H, 3CH₃, SEM), 0.08 (s, 6H, CH₃, TBDMS), 0.0 (s, 3H, CH₃), 0.13 (s, 3H, CH₃), 0.8 (s, 9H, CH₃), 0.9 (s, 9H, CH₃), 0.9-0.9 (m, 4H, 2CH₂), 1.2 (s, 3H, Me), 1.8 (bs, 1H, OH), 1.9–2.0 (m, 1H, CH₂, 2′), 2.08–2.1 (m, 1H, CH_, 2′), 2.2–2.2 (m, 1H, CH_, 2′), 2.2–2.3 (m, 1H, CH_, 2′), 2.4 (bs, 1H, OH), 2.6 (d, J = 14.5 Hz, 1H, CH₂, bridge), 2.8 (d, J = 14.5 Hz, 1H, CH₂, bridge), 3.2 (q, 2H, CH₂, base), 3.5 (t, J = 8 Hz, 4H, CH₂, SEM), 3.6 (dd, 4H, CH₂, 5′) 3.7 (m, 2H, 5′), 3.8 (bt, 2H, 4), 3.9 (bt, 1H, 4′), 4.3 (bt, 1H, 3′), 4.5 (bt, 1H, 3′), 5.1 (d, J = 10 Hz, 1H, CH₂, SEM), 5.2 (d, 1H, CH₂, SEM), 5.3–5.3 (m, 2H, CH₂, SEM), 6.2 (t, J = 7 Hz, 1H, 1′), 6.3 (t, 1H, 1′), 7.6 (s, 1H, base); ¹³C NMR (CDCl₃): δ −5.5 (CH₃), −5.3 (CH₃), −4.8 (CH₃), −4.7 (CH₃), −1.47 (CH₃), −1.43 (CH₃), 17.93 (Cquat), 18.01 (CH₃), 18.0 (CH₃), 18.3 (Cquat), 21.7 (CH₃), 25.7 (CH₃), 25.9 (CH₃), 32.0 (CH₂), 37.6 (CH₂), 41.1 (CH₂), 42.4 (Cquat), 45.0 (CH₂-base), 62.5 (CH₂), 63.3 (CH₂), 66.7 (CH₂), 67.7 (CH₂), 70.0 (CH₂), 70.3 (CH₂), 71.8 (CH), 72.8 (CH), 85.3 (CH), 86.1 (CH), 86.4 (CH), 88.2 (CH), 108.4 (Cquat), 138.9 (CH), 150.3 (Cquat), 152.9 (Cquat), 164.0 (Cquat), 173.5 (Cquat); HRMS: m/z: 973.5215 (calcd. for C₄₄ H₈₅ N₄ O₁₂ Si₄; 973.5241) (M + H); MS: (TOF, MS, ESI) m/z 996, 973, 973, 947, 946, 945, 917, 829, 801, 729.

Compound 7

Mono TBDMS dinucleoside was isolated from the deprotection reaction of 3 using 4% HF:Pyridine. Yield: 32%; white solid; R_f. 0.7; ¹H NMR (CDCl₃): δ −0.0 (s, 9H, SiCH₃), − 0.0 (s, 9H, SiCH₃), −0.06 (s, 9H, CH₃, TBDMS), 0.8 (s, 6H, SiCH₃, TBDMS), 0.8–0.9 (m, 4H, CH₂), 1.1 (s, 3H, Me, C5), 2.0-2.0 (m, 1H, CH₂, 2′), 2.1–2.2 (m, 2H, CH_, 2′), 2.3-2.3 (m, 1H, CH, 2), 2.6 (d, J = 14.5 Hz, 1H, CH₂, bridge), 2.7 (d, J = 14.5 Hz, 1H, CH₂ bridge), 3.1 (d, J = 13 Hz, 1H, CH₂, base), 3.4 (d, J = 13 Hz, 1H, CH₂, base), 3.5 (t, J = 8 Hz, 2H, CH₂, SEM), 3.6 (t, J = 9 Hz, 2H, CH₂, SEM), 3.6–3.7 (m, 3H, CH₂, 5′), 3.8 (bt, 1H, 4′), 3.9 (d, J = 11 Hz, 1H, 5′), 4.0 (bt, 1H, CH, 4′), 4.4 (bt, 1H, 3′), 4.4 (bt, 1H, 3′), 5.1-5.1 (m, 2H, CH₂, SEM), 5.2 (d, J = 10 Hz, 1H, CH₂, SEM), 5.3 (d, J = 9.5Hz, 1H, CH₂, SEM), 6.1-6.1 (m, 2H, 1), 7.8 (s, 1H, base); ¹³C NMR (CDCl₃): δ − 4.9 (CH₃), − 4.7 (CH₃), −1.5 (CH₃), 17.9 (CH₂) 18.05 (CH₂), 21.45 (CH₃), 25.6 (CH₃), 31.7 (CH₂), 37.1 (CH₂), 41.8 (CH₂), 42.4, 45.15 (CH₂-base), 61.8 (CH₂), 62.5 (CH₂), 66.9 (CH₂), 67.6 (CH₂), 69.8 (CH₂), 70.1 (CH₂), 71.7 (CH), 72.37 (CH), 85.63 (CH), 86.02 (CH), 87.52 (CH), 88.5 (CH), 107.5 (Cquat), 139.98 (CH), 150.4 (Cquat), 152.1 (Cquat), 163.9 (Cquat), 174.5 (Cquat); HRMS: m/z: 859.4369 (calcd. for C₃₈ H₇₁ N₄ O₁₂ Si₃; 859.4376) (M + H); MS: (TOF, MS, ESI) m/z 882, 881, 831, 803, 715, 687, 615, 597, 543.

3′-O-tert-butyldimethylsilyl-thymidine 14

Yield: 72%; white solid; R_f. 0.2; ¹H NMR (CDCl₃): δ −0.07 (s, 9H, TBDMS), − 0.8 (s, 6H, SiCH₃, TBDMS), 1.8 (s, 3H, Me, C5), 2.05–2.0 (m, 1H, CH₂, 2′), 2.3–2.38 (m, 1H, CH_, 2′), 3.3 (s, 1H, OH), 3.79 (d, J = 13 Hz, 1H, CH₂, 5), 3.85 (d, J = 13 Hz, 1H, CH₂, 5), 4.0 (s, 1H), 4.4 (s, 1H), 6.3 (t, 1H, 1), 7.52 (s, 1H, C6); ¹³C NMR (CDCl₃): δ 5.4 (CH₃), − 5.3 (CH₃), 12.53 (CH₃), 18.34 (CH₂) 25.9 (CH₃), 41.1 (CH₂), 63.6 (CH₂), 72.5 (CH), 85.0 (CH), 87.1 (CH), 110.9 (Cquat), 135.5 (CH), 150.6 (Cquat), 164.0 (Cquat); MS: (TOF, MS, ESI) m/z 357, 342.

5′-O-triethylsilyl-adenosine 16

A solution of adenosine 3 (0.300 g, 1.19 mmol) in DMF (3 mL) was stirred at room temperature for 5 minutes followed by dropwise addition of a solution of triethylsilyl chloride (0.163 g, 1.0 mmol) in DMF (3 mL). After complete addition the reaction mixture was stirred for 8 hours at room temperature. Upon complete triethylsilylation, the solvent was removed under reduced pressure. The residue was dissolved in methylene chloride and washed with saturated sodium bicarbonate solution. The methylene chloride layer was dried over anhydrous sodium sulfate, concentrated, and finally the residue was purified on a silica gel column (flash chromatography) using a mixture of methanol: methylene chloride (10:90), resulting in the desired product as a white fluffy solid with 85% yield. White solid; R_f. 0.2; ¹H NMR (CDCl₃): δ 0.48 (q, 6H, 3CH₂), 0.83 (t, J = 7.5 Hz, 9H, 3CH₃), 2.25–2.3 (m, 1H, CH₂, 2′), 2.6–2.7 (m, 1H, CH₂, 2′), 3.64 (dd, J = 4/7 Hz, 1H, 5), 3.75 (dd, J = 4/7 Hz, 1H, CH₂, 5′), 3.9 (d, J = 3.5 Hz, 1H), 4.3 (bt, 1H), 5.3 (d, 1H), 6.3 (t, 1H, 1′), 8.0 (s, 1H), 8.2 (s, 1H); ¹³C NMR (CDCl₃): δ 3.8 (CH₂), 6.6 (CH₂), 39.0 (CH₂) 62.8 (CH₂), 70.4 (CH), 83.3 (CH), 87.2 (CH), 119.1 (Cquat), 139.5 (CH), 149.14 (Cquat), 152.5 (CH), 156.0 (Cquat).

3′-O-tert-butyldimethylsilyl-5′-O-triethylsilyl-adenosine 17

Viscous oil; R_f. 0.5; ¹H NMR (CDCl₃): δ 0.05 (s, 6H, TBDMS), 0.59 (q, 6H, 3CH₂), 0.87 (s, 9H, TBDMS) 0.94 (t, J = 7.5 Hz, 9H, 3CH₃), 2.38–2.4 (m, 1H, CH₂, 2′), 2.5–2.6 (m, 1H, CH₂, 2′), 3.7 (dd, J = 4/7 Hz, 1H, 5′), 3.8 (dd, J = 4/7 Hz, 1H, CH₂, 5′), 3.9 (bt, 1H), 4.5 (bt, 1H), 5.3 (d, 1H), 6.32 (bs, 2H, NH₂), 6.4 (m, 1H, 1), 8.1 (s, 1H), 8.2 (s, 1H).

3′-O-tert-butyldimethylsilyl-adenosine 18

White solid; R_f. 0.3; ¹H NMR (DMSO-d₆): δ 0.0 (s, 6H, TBDMS), 0.87 (s, 9H, TBDMS) 2.2–2.3 (m, 1H, CH₂, 2′), 2.6-2.6 (m, 1H, CH₂, 2′), 3.65 (dd, J = 4/7 Hz, 1H, 5), 3.7 (dd, J = 4/7 Hz, 1H, CH₂, 5′), 3.8 (m, 1H), 4.29 (bt, 1H), 5.4 (s, 1H, OH), 6.3 (m, 1H, 1), 6.32 (bs, 2H, NH₂), 8.1 (s, 1H), 8.2 (s, 1H).

N³-Trimethylsilylethoxymethyl-thymidine 23

Yield: 76%; white solid; R_f. 0.2; ¹H NMR (CDCl₃): δ −0.05 (s, 9H, SEM), − 0.09 (t, 2H, SEM), 1.8 (s, 3H, Me, C5′), 2.3 (t, 2H, CH₂, 2′), 3.1 (bs, 1H, OH), 3.3 (bs, 1H, OH), 3.6 (t, 2H, SEM), 3.79 (d, J = 13 Hz, 1H, CH₂, 5′), 3.85 (d, J = 13 Hz, 1H, CH₂, 5′), 3.9 (bt, 1H), 4.51 (bt, 1H), 5.3 (s, 2H, SEM), 6.1 (t, 1H, 1′), 7.4 (s, 1H, C6); ¹³C NMR (CDCl₃): δ 1.4 (CH₃), 13.2 (CH₃), 18.1 (CH₂) 40.1 (CH₂), 62.1 (CH₂), 67.7, 70.1, 71.1, 86.9, 110.3 (Cquat), 135.5 (CH), 151.0 (Cquat), 163.0 (Cquat); MS: (TOF, MS, ESI) m/z 373, 372.

CONCLUSION

In summary, we describe here a simple methodology for the deprotection of TES ethers to the corresponding alcohols with control of chemoselectivity. A published method for deprotection of TES ethers using HF:pyridine resulted in low yields of the desired dinucleosides. However, we found that TES ethers are selectively deprotected to the corresponding alcohols in high yields using formic acid in methanol under mild reaction conditions. In addition, the protected 5R and 5S-dinucleosides were easily prepared and purified on a silica gel column.