Synthesis of nucleobase-functionalized morpholino-modified nucleoside monomers through palladium-catalyzed cross-coupling reactions

FULL PAPER

DOI: 10.1002/ejoc.201201384

Synthesis of Nucleobase-Functionalized Morpholino-Modified Nucleoside

Monomers Through Palladium-Catalyzed Cross-Coupling Reactions

Bappaditya Nandi,^[a]Sankha Pattanayak,^[a]Sibasish Paul,^[a]and Surajit Sinha*^[a]

Keywords: Bioorganic chemistry / Nucleosides / Modified nucleosides / Nucleotides / Halogenation / Palladium /

Cross-coupling

Morpholino-modified nucleoside analogues have wide-

spread applications in developmental biology. To achieve nu-

cleobase-functionalized forms of morpholino nucleosides,

syntheses of 5-substituted cytidine, 8-substituted adenosine,

and 8-substituted guanosine morpholino nucleoside mono-

mers are described for the first time. The syntheses are based

on the use of 5-iodocytidine, 8-bromoadenosine, and 8-

bromoguanosine morpholino nucleosides as the key starting

materials. These iodo or bromo derivatives have also been

synthesized for the first time. Palladium-mediated cross-cou-

pling reactions (Sonogashira, Suzuki, and Heck) were then

employed with the halo derivatives to accomplish the substi-

tutions. Different reaction conditions for C, A, and G were

standardized to achieve the conversions. The strategy was

devised in such a way that the useful N-trityl protecting

groups remain at the end. The catalyst combinations used for

Sonogashira, Suzuki, and Heck reactions were Pd-

(PPh₃)₂Cl₂·CuI, Pd(dppf)Cl₂·CH₂Cl₂, and Pd(OAc)₂, respec-

tively. Heck coupling between 5-iodocytidine monomer and

methyl acrylate worked well, whereas with acrylonitrile the

exocyclic amine of cytidine was found to form the aza-

Michael adduct. In this context, treatment of iodocytidine

with methyl acrylate under two different sets of conditions

was found to produce either the Michael addition product or

the Heck coupling product. Four of the functionalized

morpholino monomers have been further confirmed by sin-

gle-crystal X-ray structural analysis. All of these function-

alized monomers were obtained in good to excellent overall

yields.

nanotechnology^[9]and in surface hybridization^[10,11]as neu-

tral DNA analogues. Synthesis and applications of MO tri-

phosphates as chain-terminating reagents in DNA sequenc-

ing have been reported recently.^[12,13]In spite of the poten-

tial wide application of morpholinos, nucleobase-function-

alized forms of such compounds have yet to be explored;

whereas modified oligonucleotides in general have shown

significant antiviral^[14]or anticancer^[14b,15]activities and

bioanalytical applications,^[16]similar studies on modified

morpholino analogues are not well documented. Ideal sites

for the incorporation of any group in a nucleobase without

Introduction

Morpholino-modified (MO) antisense oligonucleotides

(Figure 1, Gene Tools LLC^[1]) are a special class of DNA

analogues extensively used for evaluating the functions of

specific genes.^[2]These reagents can block RNA splicing or

translation by targeting to the 5Ј-UTR region and have high

resistance to cellular enzymatic degradation processes.^[3,4]

They have been employed to study a range of model organ-

isms including sea urchins, zebrafish, frogs, mice, etc.^[5]

Morpholino-modified nucleotides contain regular DNA

bases with the modification of the deoxyribose rings by

morpholine rings, linked through phosphorodiamidate link-

ages (Figure 1). Modified oligonucleotides (DNA or

siRNA)^[6,7]containing single morpholino units (T- or U-

morpholino) show better efficacy for gene silencing and bet-

ter resistance towards nuclease activity.^[8]Applications of

MO oligomers are not limited only to antisense activity;

these oligomers have also found growing applications in

[a] Department of Organic Chemistry, Indian Association for the

Cultivation of Science,

2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032,

India

Fax: +91-33-24732805

E-mail: ocss5@iacs.res.in

Homepage: http://ww w .iacs.res.in/ochem/ocss5/

Supporting information for this article is available on the

WWW under http://dx.doi.org/10.1002/ejoc.201201384.

Figure 1. Structural differences between DNA and morpholino-

modified oligonucleotides.

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disturbing Watson–Crick base pair formation are the C-5 Table 1. Attempted iodination of cytidine morpholino monomer

2.^[a]

position in a pyrimidine base and the C-8 position in a pur-

ine base. Palladium-catalyzed cross-coupling reactions re-

main the methods most widely used for introduction of

various groups into these positions.^[17]

[18]

Sonogashira,

Suzuki,^[19]and Heck^[20]coupling reac-

tions have been used to prepare modified nucleosides. Many

such C-modified nucleoside triphosphates can be enzymati-

cally incorporated into oligonucleotides.^[21]The presence of

a triethylsilylethynyl group in a nucleobase is known to pro-

vide transient stability against endonucleases.^[22]Incorpora-

tion of a propyne group in a nucleobase is known to pro-

vide better duplex stability in DNA.^[23]Summerton et al.

have reported the synthesis of regular morpholino mono-

mers (A, G, C, and T) and oligomers, but no functionalized

forms of these monomers were reported in their patent.^[24]

Recently, we have reported the synthesis of functionalized

U-morpholino monomers.^[25]Here we describe the synthe-

sis of 5-substituted cytidine and 8-substituted adenosine

and guanosine morpholino monomers from the corre-

sponding halo derivatives by means of Sonogashira, Suzuki,

and Heck coupling reactions. In order to synthesize the key

starting materials we required regular morpholino mono-

mers of cytidine, adenosine, and guanosine, which were syn-

thesized by our established protocol.^[26]Because there is no

literature precedence for the synthesis of iodo-/bromo-sub-

stituted derivatives of regular morpholino monomers, we

then standardized the conditions from the available pro-

cedures for the halogenation of nucleosides or ribonucleo-

sides.

[a] Unless otherwise specified, all reactions were carried out on

0.08 mmol scales. [b] Reaction was carried out under microwave

irradiation (200 W) for 8 min. [c] Result on 0.7 mmol scale.

modification allowed us to employ widely used iodination

conditions for cytidine^[28]in acidic media. Accordingly,

iodine/iodic acid treatment in CCl₄/AcOH (1:1) afforded

the iodinated product 5 in 91% yield. After removal of the

Results and Discussion

Synthesis of the Morpholino-Modified 5-Iodocytidine

Nucleoside

Our initial attempts to iodinate cytidine morpholino nu-

cleoside 2 are described in Table 1.

Our previously established conditions for the iodination

of uridine monomer^[25]with ICl/K₂CO₃in MeOH (Table 1,

Entry 1) failed miserably to give the desired product 3: we

instead isolated the unreacted starting material 2 (20%) and

an assortment of unidentified side products. When Ag₂CO₃

was used as a base (Table 1, Entry 2) the iodo compound 3

was obtained in very poor yield along with the detritylated

monomer, unreacted starting material, and several other

unidentified side products. N-Iodosuccinimide-mediated

iodination reactions in DMF under heating or micowave

conditions^[27]were also unsatisfactory in our case (Table 1,

Entry 3). Interestingly, though, when the solvent was

changed to MeOH, a 52% yield of 3 was obtained, but on a

larger scale the yield dropped to 40% because of enhanced

detritylation (Table 1, Entry 4).

Notably, in all these cases a certain percentage of the

detritylated starting material 1 was isolated as a side prod-

uct, and so we abandoned the use of the trityl protecting

group on the morpholine component, instead deploying the

Scheme 1. Synthesis of N-trityl-protected 5-iodocytidine morphol-

acid-stable trifluoroacetyl derivative 4 (Scheme 1). This ino monomer.

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Nucleobase-Functionalized Modified Nucleoside Monomers

trifluoroacetate group and reprotection with a trityl group Table 2. Sonogashira coupling of 5-iodocytidine morpholino

monomer 3 with various terminal alkynes.^[a]

(because it is commonly used during oligomerization^[24]),

we isolated the product 3 in 81% overall yield from 1

(Scheme 1). We were also able to isolate a consistent yield

of 3 on a larger scale (10 g).

The structure of the iodo derivative 6 was confirmed by

X-ray crystal structure determination (Figure 2). In the so-

lid-state structure of 6 we observed two interesting non-

covalent interactions: halogen bond^[29]and C–H/π interac-

tions^[30](Figure S1 in the Supporting Information).

Figure 2. ORTEP view of 6 with 30% thermal ellipsoid probability.

Hydrogen atoms are omitted for clarity.

Sonogashira Coupling of the Morpholino-Modified 5-

Iodocytidine Nucleoside

With the iodo-substituted monomer 3 to hand, we at-

tempted Sonogashira coupling with various acetylenes

(Table 2). In a model reaction with phenylacetylene, the

Pd(PPh₃)₂Cl₂/CuI catalyst system in CH₂Cl₂/MeCN (2:1) at

room temperature was found to effect clean conversion with

excellent yield (Table 2, Entry 1). Use of other diversely

substituted acetylene counterparts allowed us to achieve C-

5-substituted cytidine morpholino monomers ornamented

with diversified functionalities in good to excellent yields.

Excesses (2.1–2.5 equiv.) of acetylenes were needed, due to

the formation of homocoupled acetylene byproducts. Dif-

ferent aromatic (Table 2, Entries 1–3), aliphatic (Table 2,

Entries 4–10), and heteroaromatic (Table 2, Entry 11)

acetylenes responded smoothly. Dansyl-labeled morpholino

monomer 7j might be useful as a fluorescent probe and was

synthesized in 91% yield. An X-ray crystal structure of 7j

is shown in Figure 3.

The absorption/emission spectra of 7j show an absorp-

tion maximum at 304 nm and an emission maximum at

512 nm, which corresponds to green fluorescence (Fig-

ure 4).

Ferrocene-containing cytidine morpholino monomer 7l

was synthesized and its redox behavior in CH₂Cl₂in the

potential range between 0 and +1.1 V was studied by cyclic

voltammetry (TBAP, 0.1 m) with a platinum disc as working

electrode. The potential is referenced to the saturated Ag/

AgCl electrode. A reversible oxidative response appeared

near 0.61 V (Figure 5). This higher value (relative to 0.43 in

[a] Reaction conditions: reactions were performed on 0.12–

0.2 mmol scales. [b] Isolated yields. [c] Conversion of 3 when

2.5 equiv. of cyclohexylacetylene was used. [d] Pd(PPh₃)₂Cl₂

(6 mol-%) and CuI (16 mol-%) were added. [e] DMF as solvent,

Et₃N (6 equiv.), Pd(PPh₃)₂Cl₂(6 mol-%), CuI (16 mol-%) were

the case of ferrocene/ferrocenium) is attributed to the re- used. [f] Yield based on recovered starting material.

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Suzuki Coupling of the Morpholino-Modified 5-

Iodocytidine Nucleoside

To optimize the Suzuki coupling reactions, several sets

of conditions were screened for a representative reaction be-

tween iodocytidine morpholino monomer 3 and phenyl-

boronic acid with variation of base, catalyst, solvent, and

temperature. The results are summarized in Table 3.

Table 3. Standardization of Suzuki coupling conditions.^[a]

Figure 3. ORTEP view of 7j with 30% thermal ellipsoid probability.

Hydrogen atoms are omitted for clarity.

Figure 4. UV/Vis absorption spectra (dashed line) of 7j (1.31ϫ10^–4

m in CH₂Cl₂) and fluorescence emission spectra (solid line; λ_ex

=

300 nm) of 7j (1.26ϫ10^–4m in CH₂Cl₂).

duced electron density on the cytidine-conjugated Cp ring.

Such a donor–acceptor combination in a ferrocene/cytidine

conjugate could be useful for exhibiting nonlinear optical

properties or for redox-active oligonucleotide synthesis.^[31]

Two morpholino units were also successfully coupled with

the bis(propargyl) ether of catechol to provide the bis-cou-

pled product in 46% yield (Table 2, Entry 13).

[a] Unless otherwise specified, all reactions were carried out with 3

(0.06 mmol, 1 equiv.), PhB(OH)₂(0.12 mmol, 2 equiv.), base

(3 equiv.), and catalyst (7 mol-%) in dry solvent (1–1.5 mL) under

Ar. [b] PhB(OH)₂(1.5 equiv.) was used.

Our initially attempted Suzuki reaction with Pd(PPh₃)₄

in toluene^[32]gave the desired coupling product 8a in only

12% yield, along with recovered starting material 3 and,

as the major product, the deiodinated product 2 (Table 3,

Entry 1). In DMF, none of the desired product was formed

(Table 3, Entry 2). Nor did the presence of Cs₂CO₃as a

base improve the yield of 8a (Table 3, Entry 3). The reaction

was carried out by Taylor’s procedure,^[33]in the presence of

Pd(dppf)Cl₂·CH₂Cl₂as a catalyst in THF/DMF (1:1) at

60 °C, to afford 8a as a major product in 60% yield

(Table 3, Entry 4). In order to minimize the side reaction,

the experiment was repeated in THF or DMF at room tem-

perature: in THF the yield of 8a was reduced to 36%

(Table 3, Entry 5), whereas in DMF no conversion was ob-

served (Table 3, Entry 6). Notably, however, formation of 2

was not observed in THF at room temperature. We thus

increased the temperature to 60 °C, and a pleasing 81%

Figure 5. Cyclic voltammogram of 7l in CH₂Cl₂.

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Nucleobase-Functionalized Modified Nucleoside Monomers

yield of 8a was obtained (Table 3, Entry 7). When the Heck Coupling of the Morpholino-Modified 5-Iodocytidine

amount of phenylboronic acid was reduced from 2 equiv. to Nucleoside

1.5 equiv., the yield under otherwise the same conditions

Heck coupling of 3 with methyl acrylate was performed.

dropped to 62% (Table 3, Entry 8). Use of Pd(PPh₃)₄under

The best result was obtained when dioxane was used as a

these conditions was found to be no better than use of the

solvent (Table 5).

previous catalyst (Table 3, Entry 9). A combination of

Pd(dppf)Cl₂·CH₂Cl₂, K₃PO₄, and THF was thus essential

to afford satisfactory yields.

Table 5. Optimization of Heck coupling of 3 with methyl acrylate.

We then applied the optimized conditions to several

other boronic acids, as depicted in Table 4. Substituted aryl-

boronic acids underwent high-yielding coupling to yield 5-

substituted cytidine monomers. A boronic ester also gave

the coupling product in 79% yield (Entry 7, Table 4).

Table 4. Suzuki coupling reactions between 5-iodocytidine

morpholino monomer 3 and arylboronic acids.^[a]

With acrylonitrile, no Heck coupling product was

formed under these conditions, and mostly the starting ma-

terial 3 was recovered. The combination of Pd(OAc)₂and

KOAc/nBu₄NBr^[34]was then used with acrylonitrile, but

surprisingly the Michael addition product 10 (Scheme 2)

[a] Reaction conditions: reactions were performed on 0.12–

0.15 mmol scales. [b] Isolated yields.

Scheme 2. Unexpected Michael addition product formation with

iodocytine monomer 3.

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was isolated rather than the Heck coupling product. A sim- 90 °C; this was essential because the bromo compounds are

ilar result was obtained even in the absence of Pd(OAc)₂. less reactive than their iodo counterparts. After Sonoga-

After TBDPS removal, the Michael addition product 10a shira coupling with various alkynes, we isolated a number

was also confirmed by X-ray crystal structure analysis (Fig- of 8-alkynylated adenosine morpholino monomers featur-

ure 6). Use of methyl acrylate as the Michael acceptor un- ing diverse functionalities in good yields (Table 6).

der otherwise identical reaction conditions was also found

to yield the corresponding adduct 11 (Scheme 2).

Table 6. Sonogashira coupling of 8-bromoadenosine morpholino

monomer 13.^[a]

Figure 6. ORTEP view of 10a with 30% thermal ellipsoid prob-

ability. Hydrogen atoms are omitted for clarity.

Synthesis of the Morpholino-Modified 8-Substituted

Adenosine Nucleoside

To synthesize 8-substituted morpholino-modified adenos-

ine nucleosides through Pd-catalyzed cross-coupling reac-

tions, an 8-halo-substituted adenosine monomer was re-

quired. The bromo derivative was used as the starting mate-

rial in preference to the iodo derivative because direct iodin-

ation of a purine nucleoside is not fruitful, due to the elec-

trophilic character of the C-8 center.^[35]The greater oxi-

dation potential of bromine helps bromination at this posi-

tion. The bromination was performed in Na₂HPO₄(10%)

buffer^[36]medium, to take care of the formed HBr, so that

the trityl group would survive (Scheme 3).

[a] Reaction conditions: reactions were performed on 0.12–

0.15 mmol scales. [b] Isolated yields.

We also then prepared several aryl-substituted adenosine

monomers (Table 7) through Suzuki reactions in the pres-

ence of the same catalyst/base combination as discussed

Scheme 3. Synthesis of 8-bromoadenosine morpholino monomer.

above for cytidine monomers. The reactions gave incom-

The bromo compound 13 did not undergo Sonogashira plete conversion in THF at 60 °C even for longer reaction

coupling under the conditions previously applied for cytid- times, so this solvent was replaced by 1,4-dioxane to allow

ine monomer 3 at room temperature. The conversion was the reactions to be performed at 90 °C, providing complete

achieved, however, by repeating the reaction in DMF at conversions.

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Nucleobase-Functionalized Modified Nucleoside Monomers

Table 7. Suzuki coupling reactions between 13 and arylboronic

Table 8. Attempted bromination of morpholino-modified guan-

acids.^[a]

osine monomer 16.^[a]

[a] Reaction conditions: reactions were performed on 0.8–

0.12 mmol scales.

Of these three sets of conditions, Br₂/Na₂HPO₄in diox-

ane/water was the best for G-monomer and also worked

well for A-monomer 12. Accordingly, to improve the solu-

bility of the monomer, TBDPS was removed and the reac-

tion was carried out in water/dioxane. To our delight, the

bromo derivative was obtained in very good yield

(Scheme 4).

[a] Reaction conditions: reactions were performed on 0.12–

0.15 mmol scales. [b] Isolated yields.

Under the optimized conditions for cytidine we failed to

obtain the corresponding Heck coupling product for adenos-

ine when methyl acrylate was used.

Synthesis of the Morpholino-Modified 8-Substituted

Guanosine Nucleoside

The bromination conditions used with adenosine

morpholino 12 were not satisfactory in the case of guan-

osine morpholino monomer 16: we only isolated a 24%

yield of the bromo-guanosine monomer 17 along with a

large amount of the unreacted starting material (Table 8,

Entry 1). Replacement of Na₂HPO₄with KOAc did not im-

Scheme 4. Synthesis of morpholino-modified 8-bromoguanosine

monomer 19.

The bromo compound 19 was next used for Sonogashira

prove the yield (Table 8, Entry 2). To increase the solubility, and Suzuki couplings under the conditions already opti-

the reaction was performed in MeCN in the presence of mized for adenosine, and we isolated the desired products

NBS, and a mixture of undesired products was isolated 20 and 21 (Scheme 5) in 88% and 62% yields, respectively.

(Table 8, Entry 3).

An X-ray crystal structure of 20 is shown in Figure 7.

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umn chromatography on silica gels (mesh 230–400) under nitrogen.

Thin-layer chromatography (TLC) was carried out on sheets of sil-

ica gel 60 F254 on aluminum (layer thickness 0.25 mm). Visualiza-

tion of the developed chromatogram was achieved with UV light

and/or vanillin or ceric ammonium molybdate stains. All melting

points were measured with a Gallenkamp melting point apparatus.

Infrared spectra were recorded with a FTIR instrument; the fre-

quencies are reported as wavenumbers (cm^–1). ¹H NMR and ¹³C

NMR spectra were recorded at 500 and 125 MHz, respectively.

Chemical shifts are reported in parts per million (ppm) on the delta

(δ) scale. Coupling constants are reported wherever necessary in

Hertz [Hz]. Data are reported as follows: s = singlet; d = doublet;

t = triplet; q = quartet; dd = doublet of doublets; m = multiplet;

br. = broad; app = apparent; comp = complex. HRMS was per-

formed with a QTOF I (quadrupole-hexapole-TOF) mass spec-

trometer. Solution electronic spectra were measured with a diode

array spectrophotometer. Cyclic voltammetry was carried out in

Bu₄NClO₄solution (0.1 m) with a three-electrode configuration

(platinum disc working electrode, Pt counter electrode, Ag/AgCl

reference electrode) and a PC-controlled electrochemistry system.

The E_1/2value for the ferrocenium/ferrocene couple under our ex-

perimental condition was 0.43 V. Crystallographic data for 6, 7j,

10a, and 20 are provided in Table S1 in the Supporting Infor-

mation. Single-crystal X-ray data were collected at 150 K with use

of Mo-K_α(λ = 0.7107 Å) radiation and a SMART APEX dif-

fractometer and CCD area detector. Data collection and reduction

and structure solution/refinement were carried out with the

APEX II software package.^[37]All the structures were solved by

direct methods and refined in a routine manner. The non-hydrogen

atoms were treated anisotropically. All hydrogen atoms except for

those in amine groups were geometrically fixed. CCDC-903846 (for

6), -903847 (for 7j), -903848 (for 10a), and -903849 (for 20) contain

the supplementary crystallographic data for this paper. These data

can be obtained free of charge from The Cambridge Crystallo-

graphic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.

Scheme 5. Sonogashira and Suzuki couplings of the morpholino-

modified 8-bromoguanosine monomer 19.

Morpholino-Modified 7Ј-O-TBDPS-N-(trifluoroacetyl)cytidine (4):

Freshly distilled trifluoroacetic acid anhydride (2.5 mL, 17.7 mmol,

diluted in ca. 12 mL CH₂Cl₂) was added dropwise, at ice/salt bath

temperature and under Ar, to a stirred solution of 1 (8.22 g,

17.7 mmol) in dry CH₂Cl₂(170 mL). The mixture was stirred for

45 min (monitored by TLC) without removal of the ice/salt bath.

After completion of the reaction, the reaction mixture was taken

Figure 7. ORTEP view of 20 with 30% thermal ellipsoid prob-

ability. Hydrogen atoms are omitted for clarity.

Conclusions

In summary, 5-substituted morpholino-modified cytidine

monomers and 8-substituted adenosine and morpholino- up in CHCl₃(200 mL), transferred to a separating funnel, and

washed with water (250 mL) and brine (200 mL). The organic layer

was dried with anhydrous Na₂SO₄, filtered, and concentrated in

vacuo. The solid residue was purified by flash column chromatog-

raphy on silica gel (MeOH/CH₂Cl₂5–7%) to give the product 4 as

a colorless foamy solid (9.43 g, 95%). ¹H NMR (500 MHz, CDCl₃,

mixture of rotamers): δ = 8.84 (br. s, 0.62 H), 8.45 (br. s, 0.38 H),

7.69–7.64 (comp, 4 H), 7.48–7.33 (comp, 7 H), 7.15 (br. s, 0.62 H),

6.89 (br. s, 0.38 H), 6.06 (d, J = 7.5 Hz, 0.62 H), 6.00 (d, J = 7.5 Hz,

0.38 H), 5.77 (dd, J = 9.5, 2.5 Hz, 1 H), 4.67 (d, J = 12.0 Hz, 0.62

H), 4.60 (d, J = 12.5 Hz, 0.38 H), 4.26 (d, J = 12.5 Hz, 0.38 H),

modified guanosine monomers have been synthesized for

the first time. Such functionalized monomers could be use-

ful for the synthesis of functionalized MO oligomers and

might also be potential nucleotide analogues for biomedical

applications. In this context, we also have synthesized key

compounds such as 5-iodocytidine and 8-bromoadenosine

or -guanosine for the first time. We have also standardized

two different sets of conditions to obtain either the Michael

addition product or the Heck coupling product of cytidine

monomer with methyl acrylate. Work directed towards the 4.18 (d, J = 13.0 Hz, 0.62 H), 3.89–3.81 (comp, 2.38 H), 3.74–3.70

(m, 0.62 H), 3.14 (dd, J = 13.2, 10.8 Hz, 0.62 H), 3.02–2.94 (m,

0.76 H), 2.65 (app t, J = 11.2 Hz, 0.62 H), 1.09 (s, 9 H) ppm. ¹³C

NMR (125 MHz, CDCl₃, mixture of rotamers): δ = 166.4, 166.3,

synthesis of functionalized oligomers is now underway and

results will be reported in due course.

2

156.0 (q, J_C,F= 36.5 Hz), 155.8 (q, J_C,F= 36.5 Hz), 155.21,

155.18, 139.4, 139.3, 135.54, 135.51, 135.47, 132.9, 132.8, 132.75,

132.6, 130.1, 130.0, 127.93, 127.9. 116.3 (q, ¹J_C,F= 288.0 Hz), 116.2

Experimental Section

1

General: All reagents were purchased from commercial sources and

used without further purification unless otherwise stated. Chroma-

tographic purification of products was accomplished by flash col-

(q, J_C,F= 288.0 Hz), 96.5, 96.1, 80.2, 79.7, 76.4, 76.3, 64.1, 63.6,

48.8, 47.5, 46.3, 44.2, 26.8, 26.7, 19.3, 19.2 ppm. IR (KBr): ν =

˜

3341, 2932, 2859, 1701, 1647, 1487, 1184, 1113 cm^–1. HRMS

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Nucleobase-Functionalized Modified Nucleoside Monomers

(ESI⁺): calcd. for C₂₇H₃₁N₄O₄F₃Si [M + Na] 583.1964; found

583.1960.

1668, 1626, 1489, 1105 cm^–1. HRMS (ESI⁺): calcd. for C₄₄H₄₅N₄O-

₃SiI [M + Na] 855.2203; found 855.2204.

General Procedure for Sonogashira Coupling of Morpholino-Modi-

Morpholino-Modified 7Ј-O-TBDPS-N-trifluoroacetyl-5-iodocytid-

ine (5): Iodine (2.52 g, 9.93 mmol) was added to a stirred solution

of 4 (9.25 g, 16.5 mmol) in CCl₄/CH₃COOH (1:1, 110 mL). After

the system had been heated at 40 °C, iodic acid (2.62 g, 14.9 mmol)

was added and the mixture was stirred at 40 °C for 55 h. The reac-

tion mixture was concentrated in vacuo and the residue was dis-

solved in CH₂Cl₂/CHCl₃(1:1, 300 mL). The organic phase was

washed with aqueous NaHCO₃(5%, 100 mL) and brine (100 mL).

It was dried with Na₂SO₄and the solvents were evaporated. The

solid residue was purified by flash column chromatography on sil-

ica gel (MeOH/CH₂Cl₂3–5%) to give the product 5 as a colorless

fied 7Ј-O-TBDPS-N-trityl-5-iodocytidine (3): Compound

3

(167 mg, 0.2 mmol) in dry CH₂Cl₂/CH₃CN (2:1, 3 mL) was placed

in an oven-dried round-bottomed flask. The solution was purged

with Ar for 5–10 min. Triethylamine (110 μL, 0.8 mmol), the ter-

minal acetylene (amount according to Table 2), Pd(PPh₃)₂Cl₂

(4 mg, 3 mol-%), and CuI (3 mg, 8 mol-%) were added under Ar to

the stirred solution. The resulting mixture was then stirred for a

further 1–65 h (depending on the acetylene, Table 2) at room tem-

perature. The reaction mixture was extracted with CHCl₃(60 mL),

washed sequentially with water and brine, and dried with anhy-

drous Na₂SO₄. The solvent was removed under reduced pressure,

and the solid residue was purified by flash column chromatography

on silica gel with MeOH/CH₂Cl₂. Occasionally the isolated product

required further purification by flash column chromatography on

silica gel with EtOAc/petroleum ether to remove trace amounts of

catalyst impurity to afford a colorless solid product.

1

foamy solid (10.31 g, 91%). H NMR (500 MHz, CDCl₃, mixture

of rotamers): δ = 9.38 (br. s, 0.53 H), 9.26 (br. s, 0.47 H), 7.80 (s,

0.53 H), 7.72 (s, 0.47 H), 7.69–7.63 (comp, 4 H), 7.47–7.38 (comp,

6 H), 5.86 (br. s, 0.53 H), 5.84 (br. s, 0.47 H), 5.76 (dd, J = 9.8,

2.8 Hz, 0.47 H), 5.70 (dd, J = 10.0, 2.5 Hz, 0.53 H), 4.76 (d, J =

13.0 Hz, 0.47 H), 4.57 (d, J = 13.5 Hz, 0.53 H), 4.34 (d, J =

13.0 Hz, 0.53 H), 4.12 (d, J = 13.5 Hz, 0.47 H), 3.92–3.83 (comp,

2.53 H), 3.76 (dd, J = 10.8, 6.2 Hz, 0.47 H), 3.20 (dd, J = 13.5,

11.0 Hz, 0.47 H), 3.04–2.94 (m, 1.06 H), 2.63 (dd, J = 13.0, 10.5 Hz,

0.47 H), 1.10 (s, 4.77 H), 1.09 (s, 4.23 H) ppm. ¹³C NMR

(125 MHz, CDCl₃, mixture of rotamers): δ = 164.0, 163.8, 156.1

(q, ²J_C,F= 37.7 Hz), 153.6, 153.5, 145.8, 145.6, 135.5, 135.4, 132.8,

132.61, 132.59, 132.5, 130.1, 130.03, 129.99, 127.94, 127.88, 116.2

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(phenylethynyl)cytid-

ine (7a): A colorless foamy solid (yield 87%) was isolated by flash

column chromatography on silica gel (MeOH/CH₂Cl₂1–2%). ¹H

NMR (500 MHz, CDCl₃): δ = 8.79 (br. s, 1 H), 7.60–7.27 (comp,

28 H), 7.16 (m, 3 H), 6.16 (dd, J = 9.0, 2.0 Hz, 1 H), 5.93 (br. s, 1

H), 4.28–4.26 (m, 1 H), 3.73 (dd, J = 10.8, 4.8 Hz, 1 H), 3.59 (dd,

J = 10.5, 6.0 Hz, 1 H), 3.49 (d, J = 11.0 Hz, 1 H), 3.25 (d, J =

12.0 Hz, 1 H), 1.48 (app t, J = 11.2 Hz, 1 H), 1.20 (app t, J =

10.0 Hz, 1 H), 0.96 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ

= 164.5, 153.6, 143.8, 135.60, 135.56, 133.29, 133.26, 131.5, 129.85,

129.81, 129.3, 128.8, 128.5, 127.9, 127.8, 126.4, 122.3, 95.3, 91.2,

1

(q, J_C,F= 288.0 Hz), 116.1 (q, J_C,F= 288.0 Hz), 80.3, 79.8, 76.5,

76.4, 63.9, 63.6, 57.5, 48.8, 47.0, 46.2, 43.9, 26.8, 26.7, 19.3,

19.2 ppm. IR (neat): ν = 3314, 2932, 2857, 1703, 1652, 1634, 1472,

˜

1186, 1113 cm^–1. HRMS (ESI⁺): calcd. for C₂₇H₃₀N₄O₄F₃SiI [M +

Na] 709.0931; found 709.0931.

81.9, 80.1, 77.3, 76.9, 64.8, 53.1, 50.0, 26.8, 19.3 ppm. IR (KBr): ν

˜

= 3458, 3387, 3055, 2930, 2245, 2207, 1667, 1645, 1493, 1115,

706 cm^–1. HRMS (ESI⁺): calcd. for C₅₂H₅₀N₄O₃Si [M + Na]

829.3550; found 829.3550.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-iodocytidine (3):

K₂CO₃(3.9 g, 28.2 mmol) was added to a solution of 5 (9.82 g,

14.3 mmol) in MeOH (170 mL). The resulting mixture was stirred

for 3 h at room temperature and then concentrated in vacuo, and

the residue was dissolved in CH₂Cl₂(280 mL). The organic phase

was washed carefully with water (120 mL), in order to avoid the

formation of emulsion, and dried with anhydrous Na₂SO₄, and the

solvents were evaporated. The gummy solid residue was azeo-

tropically dried by evaporation of dry CH₂Cl₂or benzene in vacuo

two to three times and finally dried under vacuum for a long time

to afford white powder 6.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(4-cyanophenylethyn-

yl)cytidine (7b): A colorless foamy solid (yield 88%) was isolated

by flash column chromatography on silica gel (MeOH/CH₂Cl₂1–

2%). ¹H NMR (500 MHz, CDCl₃): δ = 9.17 (br. s, 1 H), 7.69–7.26

(comp, 27 H), 7.16 (m, 3 H), 6.15 (dd, J = 9.2, 1.8 Hz, 1 H), 5.95

(br. s, 1 H), 4.30–4.28 (m, 1 H), 3.74 (dd, J = 10.5, 4.5 Hz, 1 H),

3.62 (dd, J = 10.5, 5.5 Hz, 1 H), 3.51 (d, J = 11.0 Hz, 1 H), 3.27

(d, J = 12.0 Hz, 1 H), 1.52 (app t, J = 11.0 Hz, 1 H), 1.20 (app t,

J = 10.2 Hz, 1 H), 0.96 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃):

δ = 164.3, 153.4, 144.8, 135.6, 135.5, 133.3, 133.2, 132.2, 131.8,

129.85, 129.8, 129.3, 127.9, 127.8, 127.1, 126.5, 118.4, 112.0, 93.6,

90.2, 84.7, 81.9, 77.3, 76.9, 64.7, 53.2, 50.0, 26.8, 19.3 ppm. IR

Triethylamine (3 mL, 21.5 mmol) and trityl chloride (4.38 g,

15.7 mmol) were added at 5 °C under Ar to a stirred suspension of

the crude product 6 in dry CH₂Cl₂(220 mL). The resulting mixture

was stirred overnight at room temperature. The reaction mixture

was taken up in chloroform (150 mL), transferred to a separating

funnel, and washed with water (250 mL) and brine (200 mL). The

organic layer was dried with anhydrous Na₂SO₄, filtered, and con-

centrated in vacuo. The solid residue was purified by flash column

chromatography on silica gel (MeOH/CH₂Cl₂2–3%) to give the

product 3 as a colorless foamy solid (10.8 g, 90%) together with

(neat): ν = 3428, 3331, 3069, 2930, 2228, 2214, 1654, 1503, 1116,

˜

910, 737 cm^–1. HRMS (ESI⁺): calcd. for C₅₃H₄₉N₅O₃Si [M + Na]

854.3502; found 854.3503.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(2-nitrophenylethyn-

yl)cytidine (7c): A colorless foamy solid (yield 94%) was isolated

by flash column chromatography on silica gel (MeOH/CH₂Cl₂1–

1

recovered starting material 6 (338 mg, 4%, recovered in 15–20% 2%). H NMR (500 MHz, CDCl₃): δ = 8.14 (d, J = 8.0 Hz, 1 H),

MeOH/CH₂Cl₂). ¹H NMR (500 MHz, CDCl₃): δ = 8.71 (br. s, 1

H), 7.60–7.28 (comp, 23 H), 7.20–7.17 (m, 3 H), 6.11 (dd, J = 9.2,

7.66 (s, 1 H), 7.61–7.28 (comp, 25 H), 7.17 (m, 3 H), 6.57 (br. s, 1

H), 6.39 (br. s, 1 H), 6.21 (dd, J = 9.2, 1.2 Hz, 1 H), 4.30–4.28 (m,

2.2 Hz, 1 H), 5.60 (br. s, 1 H), 4.27–4.24 (m, 1 H), 3.74 (dd, J = 1 H), 3.76 (dd, J = 10.8, 4.2 Hz, 1 H), 3.62 (dd, J = 10.5, 5.5 Hz,

10.5, 4.5 Hz, 1 H), 3.60 (dd, J = 10.2, 5.8 Hz, 1 H), 3.48 (d, J =

11.5 Hz, 1 H), 3.26 (d, J = 12.0 Hz, 1 H), 1.50 (app t, J = 11.0 Hz,

1 H), 1.19 (dd, J = 11.0, 9.5 Hz, 1 H), 0.98 (s, 9 H) ppm. ¹³C NMR

1 H), 3.56 (d, J = 11.0 Hz, 1 H), 3.27 (d, J = 12.0 Hz, 1 H), 1.51

(app t, J = 11.0 Hz, 1 H), 1.20 (app t, J = 10.2 Hz, 1 H), 0.97 (s,

9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 164.4, 153.3, 148.2,

(125 MHz, CDCl₃): δ = 163.7, 154.0, 146.7, 135.6, 133.3, 129.9, 145.2, 135.59, 135.56, 133.8, 133.5, 133.4, 133.3, 129.9, 129.8,

129.8, 129.4, 127.9, 127.84, 127.81, 126.5, 81.9, 77.4, 76.9, 64.7, 129.4, 128.7, 127.9, 127.8, 126.4, 125.3, 118.5, 92.1, 89.9, 89.3, 82.1,

56.2, 53.1, 50.0, 26.9, 19.3 ppm. IR (KBr): ν = 3452, 3053, 2857, 77.4, 77.0, 64.8, 53.3, 50.0, 26.9, 19.3 ppm. IR (neat): ν = 3443,

˜

Eur. J. Org. Chem. 2013, 1271–1286

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1279

B. Nandi, S. Pattanayak, S. Paul, S. Sinha

FULL PAPER

3069, 2930, 2205, 1667, 1649, 1607, 1524, 1503, 1120 cm^–1. HRMS

(ESI⁺): calcd. for C₅₂H₄₉N₅O₅Si [M + Na] 874.3401; found

874.3402.

1116, 706 cm^–1. HRMS (ESI⁺): calcd. for C₄₇H₄₈N₄O₄Si [M + Na]

783.3342; found 783.3343.

Morpholino-Modified

7Ј-O-TBDPS-N-trityl-5-(1-hydroxybut-3-

ynyl)cytidine (7h): A colorless solid (yield 86%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂3–

3.5%). ¹H NMR (500 MHz, CDCl₃): δ = 8.36 (br. s, 1 H), 7.59–

7.26 (comp, 23 H), 7.15 (m, 3 H), 6.33 (br. s, 1 H), 6.11 (d, J =

9.0 Hz, 1 H), 4.27–4.25 (m, 1 H), 3.77–3.68 (m, 3 H), 3.56 (dd, J

= 10.5, 6.0 Hz, 1 H), 3.43 (d, J = 11.0 Hz, 1 H), 3.26 (d, J =

11.5 Hz, 1 H), 2.60 (t, J = 6.0 Hz, 2 H), 2.46 (t, J = 6.2 Hz, 1 H),

1.43 (app t, J = 11.0 Hz, 1 H), 1.16 (app t, J = 10.2 Hz, 1 H), 0.97

(s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 165.0, 153.9,

142.8, 135.60, 135.58, 133.33, 133.26, 129.9, 129.8, 129.3, 127.9,

127.8, 126.5, 94.2, 91.8, 81.8, 77.3, 75.0, 72.9, 66.7, 60.7, 53.0, 50.1,

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(cyclohexylethynyl)-

cytidine (7d): An off-white foamy solid (yield 68%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂1–2%).

¹H NMR (500 MHz, CDCl₃): δ = 7.84 (br. s, 1 H), 7.59–7.27

(comp, 23 H), 7.17 (m, 3 H), 6.15 (dd, J = 9.0, 2.0 Hz, 1 H), 5.71

(br. s, 1 H), 4.26–4.24 (m, 1 H), 3.72 (dd, J = 10.5, 4.5 Hz, 1 H),

3.57 (dd, J = 10.8, 5.8 Hz, 1 H), 3.45 (d, J = 11.0 Hz, 1 H), 3.23

(d, J = 11.5 Hz, 1 H), 2.53–2.50 (m, 1 H), 1.83–1.81 (m, 2 H), 1.69–

1.65 (m, 2 H), 1.54–1.42 (comp, 4 H), 1.34–1.26 (comp, 3 H), 1.19

(app t, J = 10.0 Hz, 1 H), 0.96 (s, 9 H) ppm. ¹³C NMR (125 MHz,

CDCl₃): δ = 164.8, 153.7, 143.0, 135.6, 133.4, 129.84, 129.8, 129.4,

127.9, 127.83, 127.82, 126.4, 100.8, 91.7, 81.9, 77.3, 77.0, 71.2, 53.0,

26.9, 23.8, 23.6, 19.3 ppm. IR (KBr): ν = 3335, 2928, 2857, 2232,

˜

1647, 1505, 1105 cm^–1. HRMS (ESI⁺): calcd. for C₄₈H₅₀N₄O₄Si [M

+ Na] 797.3499; found 797.3499.

50.0, 32.7, 30.0, 26.0, 25.8, 25.1, 19.3 ppm. IR (KBr): ν = 3457,

˜

3055, 2930, 2855, 2246, 1665, 1647, 1503, 1105 cm^–1. HRMS

(ESI⁺): calcd. for C₅₂H₅₆N₄O₃Si [M + Na] 835.4019; found

835.4019.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(N-trifluoroacetyl-1-

aminoprop-2-ynyl)cytidine (7i): An off-white foamy solid (yield

88%) was isolated by flash column chromatography on silica gel

(MeOH/CH₂Cl₂2–3%). ¹H NMR (500 MHz, CDCl₃): δ = 8.04 (br.

s, 1 H), 7.58–7.23 (comp, 24 H), 7.15–7.12 (m, 3 H), 6.06 (dd, J =

9.0, 1.5 Hz, 1 H), 5.97 (br. s, 1 H), 4.25–4.20 (m, 2 H), 4.05 (dd, J

= 17.8, 4.2 Hz, 1 H), 3.72 (dd, J = 10.8, 4.8 Hz, 1 H), 3.53 (dd, J

= 10.5, 6.0 Hz, 1 H), 3.43 (d, J = 11.0 Hz, 1 H), 3.28 (d, J =

11.5 Hz, 1 H), 1.41 (app t, J = 11.2 Hz, 1 H), 1.13 (app t, J =

10.2 Hz, 1 H), 0.96 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ

Morpholino-Modified 7Ј-O-TBDPS-N-trityl- 5-(1-octanyl)cytidine

(7e): An off-white foamy solid (yield 67%) was isolated by flash

column chromatography on silica gel (MeOH/CH₂Cl₂1–2%). ¹H

NMR (500 MHz, CDCl₃): δ = 8.33 (br. s, 1 H), 7.59–7.27 (comp,

23 H), 7.16 (m, 3 H), 6.14 (d, J = 8.5 Hz, 1 H), 5.76 (br. s, 1 H),

4.26–4.24 (m, 1 H), 3.71 (dd, J = 10.5, 4.5 Hz, 1 H), 3.56 (dd, J =

10.5, 5.5 Hz, 1 H), 3.44 (d, J = 11.0 Hz, 1 H), 3.24 (d, J = 11.5 Hz,

1 H), 2.34 (t, J = 7.2 Hz, 2 H), 1.53–1.16 (comp, 9 H), 1.44 (app t,

J = 11.0 Hz, 1 H), 0.95 (s, 9 H), 0.87 (t, J = 6.8 Hz, 3 H) ppm. ¹³C

NMR (125 MHz, CDCl₃): δ = 164.9, 153.7, 143.0, 135.6, 133.3,

129.82, 129.77, 129.4, 127.9, 127.8, 126.4, 96.7, 91.7, 81.8, 77.2,

76.9, 71.4, 64.7, 53.0, 50.0, 31.4, 28.8, 28.7, 26.8, 22.6, 19.6, 19.3,

2

= 164.6, 157.3 (q, J_C,F= 37.7 Hz), 153.9, 144.5, 135.6, 135.56,

133.3, 133.2, 129.9, 129.8, 129.3, 127.9, 127.86, 126.6, 115.8 (q,

¹J_C,F= 286.8 Hz), 90.2, 89.9, 82.1, 77.5, 76.9, 75.2, 64.6, 53.2, 50.2,

30.3, 26.9, 19.3 ppm. IR (neat): ν = 3187, 3057, 2859, 2236, 1719,

˜

1651, 1505, 1163 cm^–1. HRMS (ESI⁺): calcd. for C₄₉H₄₈N₅O₄F₃Si

[M + Na] 878.3325; found 878.3326.

14.1 ppm. IR (neat): ν = 3458, 3317, 3057, 2930, 2857, 2242, 1667,

˜

1651, 1505, 1105 cm^–1. HRMS (ESI⁺): calcd. for C₅₂H₅₈N₄O₃Si [M

+ Na] 837.4176; found 837.4175.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(N-dansyl-1-amino-

prop-2-ynyl)cytidine (7j): The reaction was carried out in the dark.

A pale greenish-yellow crystalline solid (yield 91%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂2–3%),

m.p. 209–210 °C. ¹H NMR (500 MHz, CDCl₃): δ = 8.39 (d, J =

8.5 Hz, 1 H), 8.29–8.25 (m, 2 H), 7.57–7.01 (comp, 30 H), 6.27 (br.

s, 1 H), 6.08 (dd, J = 9.0, 1.5 Hz, 1 H), 5.96 (br. s, 1 H), 4.26–4.24

(m, 1 H), 3.88 (br. s, 2 H), 3.70 (dd, J = 10.2, 4.2 Hz, 1 H), 3.53

(dd, J = 10.5, 6.0 Hz, 1 H), 3.46 (d, J = 11.0 Hz, 1 H), 3.25 (d, J

= 12.0 Hz, 1 H), 2.63 (s, 6 H), 1.45 (app t, J = 11.0 Hz, 1 H), 1.21

(app t, J = 10.2 Hz, 1 H), 0.94 (s, 9 H) ppm. ¹³C NMR (125 MHz,

CDCl₃): δ = 164.1, 153.4, 151.9, 143.6, 135.63, 135.58, 134.8, 133.4,

133.3, 130.7, 130.2, 130.1, 129.9, 129.8, 129.4, 128.7, 128.0, 127.84,

127.82, 126.5, 123.3, 118.9, 115.3, 90.5, 89.9, 81.8, 77.4, 76.9, 74.8,

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(trimethylsilylethyn-

yl)cytidine (7f): A colorless foamy solid (yield 89%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂1–2%).

¹H NMR (500 MHz, CDCl₃): δ = 8.41 (br. s, 1 H), 7.59–7.27

(comp, 23 H), 7.16 (m, 3 H), 6.13 (dd, J = 9.2, 1.8 Hz, 1 H), 5.78

(br. s, 1 H), 4.26–4.24 (m, 1 H), 3.71 (dd, J = 10.5, 4.5 Hz, 1 H),

3.58 (dd, J = 10.8, 5.2 Hz, 1 H), 3.46 (d, J = 11.0 Hz, 1 H), 3.23

(d, J = 11.5 Hz, 1 H), 1.48 (app t, J = 11.0 Hz, 1 H), 1.17 (dd, J

= 11.0, 9.5 Hz, 1 H), 0.96 (s, 9 H), 0.20 (s, 9 H) ppm. ¹³C NMR

(125 MHz, CDCl₃): δ = 164.6, 153.5, 144.4, 135.6, 133.34, 133.27,

129.9, 129.8, 129.3, 127.9, 127.84, 127.81, 126.5, 101.3, 95.8, 91.1,

82.0, 77.4, 77.0, 64.7, 53.1, 50.0, 26.9, 19.3, 0.0 ppm. IR (neat): ν

˜

= 3460, 2959, 2857, 2153, 1667, 1505, 1105 cm^–1. HRMS (ESI⁺):

calcd. for C₄₉H₅₄N₄O₃Si₂[M + Na] 825.3632; found 825.3631.

64.6, 53.1, 50.2, 45.3, 33.4, 26.9, 19.3 ppm. IR (neat): ν = 3399,

˜

3341, 3055, 2928, 2855, 2230, 1668, 1641, 1595, 1501, 1323, 1144,

1105 cm^–1. HRMS (ESI⁺): calcd. for C₅₉H₆₀N₆O₅SiS [M + Na]

1015.4013; found 1015.4012.

Morpholino-Modified

7Ј-O-TBDPS-N-trityl-5-(1-hydroxyprop-2-

ynyl)cytidine (7g): A colorless solid (yield 70%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂3–4%).

¹H NMR (500 MHz, [D₆]DMSO): δ = 7.82 (br. s, 1 H), 7.55–7.31

(comp, 23 H), 7.21 (m, 3 H), 5.88 (br. s, 1 H), 6.04 (d, J = 9.0 Hz,

1 H), 5.15 (t, J = 5.5 Hz, 1 H), 4.32–4.30 (m, 1 H), 4.22 (d, J =

6.0 Hz, 2 H), 3.73 (dd, J = 10.2, 4.2 Hz, 1 H), 3.62 (dd, J = 10.5,

6.0 Hz, 1 H), 3.23 (d, J = 10.5 Hz, 1 H), 3.17 (d, J = 11.5 Hz, 1

H), 1.44 (app t, J = 11.0 Hz, 1 H), 1.18 (app t, J = 10.2 Hz, 1 H),

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(2-pyridylethynyl)-

cytidine (7k): An off-white foamy solid (yield 90%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂2.5–

3.5%). ¹H NMR (500 MHz, CDCl₃): δ = 8.59 (br. s, 1 H), 8.54 (d,

J = 4.0 Hz, 1 H), 7.62–7.16 (comp, 29 H), 6.17 (dd, J = 8.8, 1.8 Hz,

1 H), 6.17 (br. s, overlapped, 1 H), 4.29–4.27 (m, 1 H), 3.75 (dd, J

= 10.8, 4.8 Hz, 1 H), 3.57 (dd, J = 10.8, 6.2 Hz, 1 H), 3.48 (d, J =

0.90 (s, 9 H) ppm. ¹³C NMR (125 MHz, [D₆]DMSO): δ = 164.8, 11.5 Hz, 1 H), 3.29 (d, J = 11.5 Hz, 1 H), 1.42 (app t, J = 11.0 Hz,

153.2, 144.0, 135.62, 135.56, 133.37, 133.35, 130.5, 129.5, 128.4, 1 H), 1.19 (dd, J = 10.8, 9.8 Hz, 1 H), 0.97 (s, 9 H) ppm. ¹³C NMR

126.9, 95.8, 90.3, 81.4, 76.9, 76.6, 76.0, 64.9, 53.0, 50.3, 50.0, 27.2, (125 MHz, CDCl₃): δ = 164.2, 153.3, 150.0, 145.1, 142.5, 136.2,

19.4 ppm. IR (KBr): ν = 3391, 3347, 3055, 2857, 2226, 1645, 1505,

135.46, 135.43, 133.18, 133.15, 129.8, 129.7, 129.2, 127.8, 127.71,

˜

1280

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Eur. J. Org. Chem. 2013, 1271–1286

Nucleobase-Functionalized Modified Nucleoside Monomers

127.69, 126.6, 126.4, 123.0, 94.4, 90.0, 81.7, 80.4, 77.2, 76.8, 64.6,

lapped), 129.2, 128.5, 127.9, 127.7, 126.4, 108.6, 81.6, 77.2, 77.0,

53.1, 50.1, 26.8, 19.2 ppm. IR (KBr): ν = 3458, 3331, 3055, 2930,

64.7, 53.0, 50.2, 26.8, 19.3 ppm. IR (neat): ν = 3320, 3068, 2930,

˜

2214, 1667, 1645, 1495, 1113, 708 cm^–1. HRMS (ESI⁺): calcd. for

C₅₁H₄₉N₅O₃Si [M + Na] 830.3502; found 830.3503.

1640, 1620, 1479, 1105 cm^–1. HRMS (ESI⁺): calcd. for

C₅₀H₅₀N₄O₃Si [M + Na] 805.3550; found 805.3550.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(ferrocenylethynyl)-

cytidine (7l): The general procedure with slight modifications (de-

scribed in Table 2, Entry 12) was employed. An off-white solid

(yield 84%) was isolated by flash column chromatography on silica

Morpholino-Modified

7Ј-O-TBDPS-N-trityl-5-(4-methylphenyl)-

cytidine (8b): An off-white foamy solid (yield 75%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂1.5–

2.5%). ¹H NMR (500 MHz, CDCl₃): δ = 8.76 (br. s, 1 H), 7.58–

gel (MeOH/CH₂Cl₂2–3%). ¹H NMR (500 MHz, CDCl₃): δ = 8.29 7.04 (comp, 30 H), 6.21 (dd, J = 9.0, 2.0 Hz, 1 H), 5.24 (br. s, 1

(br. s, 1 H), 7.60–7.28 (comp, 23 H), 7.16 (br. s, 3 H), 6.17 (d, J =

9.0 Hz, 1 H), 5.82 (br. s, 1 H), 4.42 (s, 2 H), 4.28–4.24 (m, 1 H),

4.24 (s, 2 H), 4.18 (s, 5 H), 3.73 (dd, J = 10.5, 4.0 Hz, 1 H), 3.59

(dd, J = 10.0, 5.5 Hz, 1 H), 3.48 (d, J = 11.0 Hz, 1 H), 3.25 (d, J

= 11.5 Hz, 1 H), 1.48 (app t, J = 11.0 Hz, 1 H), 1.22 (app t, J =

10.2 Hz, 1 H), 0.97 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ =

164.5, 153.6, 142.9, 135.6, 133.3, 133.28, 129.9, 129.8, 129.4, 127.9,

127.85, 127.82, 126.5, 94.8, 91.9, 81.9, 77.4, 77.0, 76.3, 71.4, 70.1,

H), 4.26–4.24 (m, 1 H), 3.68 (dd, J = 11.0, 4.5 Hz, 1 H), 3.51 (dd,

J = 10.5, 6.0 Hz, 1 H), 3.47 (d, J = 11.5 Hz, 1 H), 3.24 (d, J =

11.5 Hz, 1 H), 2.34 (s, 3 H), 1.40 (app t, J = 11.0 Hz, 1 H), 1.24

(app t, J = 10.5 Hz, 1 H), 0.91 (s, 9 H) ppm. ¹³C NMR (125 MHz,

CDCl₃): δ = 164.2, 154.8, 139.3, 138.4, 135.6, 135.57, 133.38,

133.35, 130.2, 130.1, 129.8, 129.7, 129.4, 129.1, 127.9, 127.77,

127.75, 126.4, 108.4, 81.6, 77.2, 77.0, 64.7, 53.0, 50.2, 26.8, 21.3,

19.3 ppm. IR (neat): ν = 3292, 3055, 2928, 1660, 1649, 1487,

˜

69.2, 64.8, 64.1, 53.1, 50.0, 26.9, 19.3 ppm. IR (neat): ν = 3455,

1105 cm^–1. HRMS (ESI⁺): calcd. for C₅₁H₅₂N₄O₃Si [M + Na]

819.3706; found 819.3707.

˜

3057, 2930, 2210, 1685, 1647, 1501, 1107, 754 cm^–1. HRMS (ESI⁺):

calcd. for C₅₆H₅₄N₄O₃SiFe [M + Na] 937.3212; found 937.3214.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(4-methoxylphenyl)-

cytidine (8c): An off-white foamy solid (yield 78%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂1.5–

2.5%). ¹H NMR (500 MHz, CDCl₃): δ = 8.28 (br. s, 1 H), 7.54 (d,

J = 7.0 Hz, 2 H), 7.50–7.06 (comp, 26 H), 6.87 (d, J = 8.5 Hz, 2

H), 6.20 (dd, J = 9.0, 2.0 Hz, 1 H), 5.26 (br. s, 1 H), 4.26–4.24 (m,

Sonogashira Bis-Coupled Product 7m of 3 with the Bis(propargyl)

Ether of Catechol: The general procedure with slight modifications

(described in Table 2, Entry 13) was employed. An off-white solid

(yield 46%, based on recovered 3) was isolated by flash column

chromatography on silica gel (MeOH/CH₂Cl₂2–3%). ¹H NMR

(500 MHz, CDCl₃): δ = 7.58–7.16 (comp, 55 H), 6.58 (dd, J = 8.5, 1 H), 3.79 (s, 3 H), 3.69 (dd, J = 10.5, 4.5 Hz, 1 H), 3.52 (dd, J =

1.5 Hz, 2 H), 6.53 (br. s, 1 H), 6.14 (d, J = 8.5 Hz, 2 H), 5.61 (br.

s, 2 H), 4.79 (br. s, 4 H), 4.27–4.25 (m, 2 H), 3.72 (dd, J = 10.5,

4.5 Hz, 2 H), 3.56 (dd, J = 10.8, 5.8 Hz, 2 H), 3.46 (d, J = 11.0 Hz,

10.5, 6.0 Hz, 1 H), 3.46 (d, J = 11.0 Hz, 1 H), 3.24 (d, J = 12.0 Hz,

1 H), 1.41 (app t, J = 11.0 Hz, 1 H), 1.24 (app t, J = 10.5 Hz, 1

H), 0.91 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 164.5,

2 H), 3.25 (d, J = 11.5 Hz, 2 H), 1.43 (app t, J = 12.0 Hz, 2 H), 1.14 159.8, 154.8, 139.0, 135.57, 135.54, 133.34, 133.31, 130.5, 129.8,

(app t, J = 10.2 Hz, 2 H), 0.96 (s, 18 H) ppm. ¹³C NMR (125 MHz,

CDCl₃): δ = 164.4, 158.9, 153.4, 145.0, 135.63, 135.61, 133.4, 133.3,

130.4, 129.9, 129.8, 129.4, 128.0, 127.8, 126.5, 107.9, 103.1, 90.2,

89.7, 81.9, 78.7, 77.4, 77.0, 64.7, 56.7, 53.2, 50.1, 26.9, 19.3 ppm.

129.7, 129.4, 127.9, 127.7, 126.4, 125.3, 114.8, 108.2, 81.6, 77.1,

76.9, 64.7, 55.5, 52.9, 50.2, 26.8, 19.3 ppm. IR (neat): ν = 3470,

˜

3316, 3071, 2930, 1661, 1651, 1645, 1512, 1487, 1246, 1105 cm^–1.

HRMS (ESI⁺): calcd. for C₅₁H₅₂N₄O₄Si [M + Na] 835.3656; found

835.3570.

IR (neat): ν = 3312, 3056, 2928, 2228, 1647, 1593, 1489, 1146,

˜

1105 cm^–1. HRMS (ESI⁺): calcd. for C₉₉¹³CH₉₈N₈O₈Si₂[M + Na]

1618.6977; found 1618.6974.

Morpholino-Modified

7Ј-O-TBDPS-N-trityl-5-(4-fluorophenyl)-

cytidine (8d): An off-white foamy solid (yield 80%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂1.5–

2.5%). ¹H NMR (500 MHz, CDCl₃): δ = 8.73 (br. s, 1 H), 7.54–

7.00 (comp, 30 H), 6.17 (d, J = 9.0 Hz, 1 H), 5.30 (br. s, 1 H), 4.26–

4.24 (m, 1 H), 3.69 (dd, J = 10.2, 4.2 Hz, 1 H), 3.54 (dd, J = 10.0,

6.0 Hz, 1 H), 3.46 (d, J = 11.0 Hz, 1 H), 3.24 (d, J = 11.5 Hz, 1

H), 1.44 (app t, J = 11.0 Hz, 1 H), 1.22 (app t, J = 10.2 Hz, 1 H),

0.90 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 164.3, 162.7

(¹J_C,F= 247.8 Hz), 154.7, 139.4, 135.57, 135.52, 133.4, 133.3, 131.2

(³J_C,F= 8.8 Hz), 129.8, 129.7, 129.4, 129.1 (⁴J_C,F= 2.3 Hz), 127.9,

127.74, 127.72, 126.4, 116.4 (²J_C,F= 21.4 Hz), 107.6, 81.6, 77.1,

General Procedure for Suzuki Coupling of Morpholino-Modified 7Ј-

O-TBDPS-N-trityl-5-iodocytidine (3): K₃PO₄(3 m in H₂O, 150 μL,

0.45 mmol), the arylboronic acid/ester (0.3 mmol), and Pd(dppf)-

Cl₂·CH₂Cl₂(9 mg, 0.011 mmol) were added under Ar to a stirred

solution of 3 (125 mg, 0.15 mmol) in dry THF (2.5 mL). The re-

sulting mixture was heated at 60 °C for 6–12 h (depending on the

boronic acid, Table 4). The reaction mixture was concentrated in

vacuo and the residue was dissolved in CHCl₃(50 mL). The or-

ganic phase was washed with water and brine and dried with anhy-

drous Na₂SO₄. The solvent was removed under reduced pressure,

and the solid residue was purified by flash column chromatography

on silica gel with MeOH/CH₂Cl₂. Occasionally the isolated product

needed further purification by flash column chromatography on

silica gel with EtOAc/petroleum ether to remove trace catalyst im-

purity to afford a colorless solid product.

77.0, 64.7, 52.9, 50.1, 26.8, 19.3 ppm. IR (neat): ν = 3315, 3069,

˜

2930, 2857, 1657, 1649, 1489, 1107 cm^–1. HRMS (ESI⁺): calcd. for

C₅₀H₄₉N₄O₃FSi [M + Na] 823.3456; found 823.3456.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(4-trifluoromethoxy-

phenyl)cytidine (8e): An off-white foamy solid (yield 81%) was iso-

lated by flash column chromatography on silica gel (MeOH/

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(phenyl)cytidine (8a):

1

A colorless foamy solid (yield 81%) was isolated by flash column

CH₂Cl₂1.5–2.5%). H NMR (500 MHz, CDCl₃): δ = 8.82 (br. s, 1

1

chromatography on silica gel (MeOH/CH₂Cl₂2–2.5%). H NMR H), 7.54–7.12 (comp, 30 H), 6.17 (d, J = 10.0 Hz, 1 H), 5.33 (br. s,

(500 MHz, CDCl₃): δ = 8.17 (br. s, 1 H), 7.54–7.13 (comp, 31 H),

6.20 (dd, J = 9.0, 1.5 Hz, 1 H), 5.26 (br. s, 1 H), 4.26–4.24 (m, 1

H), 3.68 (dd, J = 10.5, 4.5 Hz, 1 H), 3.52 (dd, J = 10.5, 6.0 Hz, 1

H), 3.48 (d, J = 11.0 Hz, 1 H), 3.24 (d, J = 11.5 Hz, 1 H), 1.42

(app t, J = 11.2 Hz, 1 H), 1.24 (app t, J = 10.2 Hz, 1 H), 0.90 (s,

9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 164.2, 154.7, 139.4,

135.6, 135.56, 133.3, 133.2, 129.8, 129.7, 129.4, 129.36 (over-

1 H), 4.26–4.24 (m, 1 H), 3.69 (dd, J = 10.5, 4.0 Hz, 1 H), 3.55

(dd, J = 10.4, 5.8 Hz, 1 H), 3.47 (d, J = 11.0 Hz, 1 H), 3.24 (d, J

= 11.5 Hz, 1 H), 1.46 (app t, J = 11.0 Hz, 1 H), 1.22 (app t, J =

10.0 Hz, 1 H), 0.90 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ

= 164.0, 154.6, 149.2, 139.7, 135.56, 135.5, 133.33, 133.26, 131.9,

130.9, 129.8, 129.7, 129.4, 127.9, 127.74, 127.72, 126.4, 121.9, 120.5

(q, ¹J_C,F= 286.3 Hz), 107.3, 81.7, 77.2, 77.0, 64.7, 53.0, 50.1, 26.8,

Eur. J. Org. Chem. 2013, 1271–1286

www.eurjoc.org

1281

B. Nandi, S. Pattanayak, S. Paul, S. Sinha

FULL PAPER

19.3 ppm. IR (neat): ν = 3296, 3067, 2930, 1647, 1489, 1256 cm^–1.

17.8 ppm. IR (neat): ν = 3335, 3071, 2930, 2247, 1659, 1651, 1611,

˜

HRMS (ESI⁺): calcd. for C₅₁H₄₉N₄O₄F₃Si [M + Na] 889.3373;

found 889.3374.

1549, 1493, 1105 cm^–1. HRMS (ESI⁺): calcd. for C₄₇H₄₈N₅O₃SiI

[M + Na] 908.2469; found 908.2469.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-(1-naphthyl)cytidine

(8f): An off-white foamy solid (yield 87%) was isolated by flash

column chromatography on silica gel (MeOH/CH₂Cl₂1.5–2.5%).

nBu₄NF (0.4 mL, 0.4 mmol, 1 m in THF) was added dropwise un-

der Ar to a stirred solution of 10 (220 mg, 0.25 mmol) in dry THF.

The mixture was stirred for 4 h at room temperature. The reaction

¹H NMR (500 MHz, CDCl₃, mixture of rotamers): δ = 8.46 (br. s, mixture was concentrated in vacuo and the residue was dissolved

1 H), 7.89–7.85 (m, 2 H), 7.55–7.06 (comp, 31 H), 6.23–6.18 (m, 1 in CHCl₃(60 mL). The organic layer was washed with water and

H), 4.82 (br. m, 1 H), 4.24–4.22 (m, 1 H), 3.68–3.60 (m, 1 H), 3.50–

brine and dried with anhydrous Na₂SO₄. The solvent was removed

3.41 (m, 2 H), 3.21 (d, J = 12.0 Hz, 1 H), 1.36 (app t, J = 11.2 Hz, under reduced pressure, and the solid residue was purified by flash

1 H), 1.26–1.23 (m, 1 H), 0.86 and 0.84 (2ϫs, 9 H) ppm. ¹³C NMR

(125 MHz, CDCl₃, mixture of rotamers): δ = 164.7, 154.9, 140.5,

140.3, 135.6, 135.5, 135.4, 134.0, 133.3, 133.2, 132.2, 129.8, 129.7,

column chromatography on silica gel (MeOH/CH₂Cl₂3–4%) to

give the product 10a as a colorless solid (105 mg, 90%). H NMR

(500 MHz, [D₆]DMSO): δ = 7.80 (s, 1 H), 7.42–7.30 (comp, 12 H),

1

129.64, 129.57, 129.5, 129.4, 129.0, 128.9, 128.7, 128.6, 127.8, 7.19 (br. s, 3 H), 5.99 (d, J = 9.0 Hz, 1 H), 5.74 (s, 1 H), 4.73 (t, J

127.7, 127.64, 127.57, 127.2, 126.9, 126.6, 126.5, 126.4, 125.8, = 6.0 Hz, 1 H), 4.17–3.15 (m, 1 H), 3.56–3.46 (m, 2 H), 3.40 (t, J

125.6, 125.3, 125.1, 106.4, 106.3, 81.7, 81.5, 77.2, 77.0, 76.9, 64.6,

53.1, 53.0, 50.1, 26.8, 19.2 ppm. IR (neat): ν = 3466, 3057, 2930,

= 5.0 Hz, 2 H), 3.24 (d, J = 11.0 Hz, 1 H), 3.01 (d, J = 12.0 Hz, 1

H), 2.77 (t, J = 6.8 Hz, 2 H), 1.42 (app t, J = 11.0 Hz, 1 H), 1.21

˜

1670, 1650, 1495, 1109 cm^–1. HRMS (ESI⁺): calcd. for (app t, J = 10.0 Hz, 1 H) ppm. ¹³C NMR (125 MHz, [D₆]DMSO):

C₅₄H₅₂N₄O₃Si [M + Na] 855.3706; found 855.3707.

δ = 161.7, 153.3, 146.8, 129.5, 128.4, 126.9, 119.6, 81.7, 77.5, 76.9,

62.6, 58.4, 52.8, 49.7, 37.8, 17.2 ppm. IR (KBr): ν = 3389, 3055,

˜

Heck Coupling of Morpholino-Modified 7Ј-O-TBDPS-N-trityl-5-

iodocytidine (3) with Methyl Acrylate to Afford Compound 9:

Methyl acrylate (110 μL, 1.2 mmol), triethylamine (84 μL,

2821, 2249, 1651, 1609, 1545, 1491 cm^–1. HRMS (ESI⁺): calcd. for

C₃₁H₃₀N₅O₃I [M + Na] 670.1291; found 670.1292.

0.6 mmol), Pd(OAc)₂(3.3 mg, 0.015 mmol), and PPh₃(8 mg, Aza-Michael Addition Product 11: Methyl acrylate (130 μL,

0.03 mmol) were added under Ar to a stirred solution of 3 (125 mg,

0.15 mmol) in dry dioxane (2.5 mL). The resulting mixture was

stirred and heated at 90 °C for 5 h. The reaction mixture was con-

centrated in vacuo and the residue was dissolved in CHCl₃(50 mL).

The organic phase was washed with water and brine and dried

with anhydrous Na₂SO₄. The solvent was removed under reduced

pressure, and the solid residue was purified by flash column

chromatography on silica gel (MeOH/CH₂Cl₂2–3%) to give the

product 9 as a colorless foamy solid (98 mg, 83%). ¹H NMR

(500 MHz, CDCl₃): δ = 8.92 (br. s, 1 H), 7.58–7.13 (comp, 28 H),

6.17 (dd, J = 9.5, 2.0 Hz, 1 H), 5.81 (d, J = 15.5 Hz, 1 H), 4.27–

1.44 mmol), KOAc (44 mg, 0.45 mmol), and nBu₄NBr (64 mg,

0.2 mmol) were added under Ar to a stirred solution of 3 (150 mg,

0.18 mmol) in dry DMF (1.5 mL). The resulting mixture was

stirred and heated at 80 °C for 5 h. The reaction mixture was con-

centrated in vacuo and the residue was dissolved in EtOAc (50 mL).

The organic phase was washed with water and brine and dried

with anhydrous Na₂SO₄. The solvent was removed under reduced

pressure and the solid residue was purified by flash column

chromatography on silica gel (MeOH/CH₂Cl₂1–2%) to give the

product 11 as a colorless foamy solid (152 mg, 92%). ¹H NMR

(500 MHz, CDCl₃): δ = 7.58–7.27 (comp, 23 H), 7.18–7.15 (m, 3

4.25 (m, 1 H), 3.75 (dd, J = 10.5, 4.5 Hz, 1 H), 3.61 (s, 3 H) 3.59 H), 6.15–6.14 (m, 2 H), 4.27–4.23 (m, 1 H), 3.75–3.70 (m, 3 H),

(dd, J = 10.8, 6.2 Hz, 1 H), 3.46 (d, J = 11.5 Hz, 1 H), 3.28 (d, J

= 12.0 Hz, 1 H), 1.43 (app t, J = 11.0 Hz, 1 H), 1.13 (app t, J =

3.69 (s, 3 H), 3.58 (dd, J = 10.5, 6.0 Hz, 1 H), 3.50 (d, J = 11.5 Hz,

1 H), 3.24 (d, J = 12.0 Hz, 1 H), 2.61 (t, J = 5.8 Hz, 2 H), 1.47

10.2 Hz, 1 H), 0.96 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ (app t, J = 11.0 Hz, 1 H), 1.17 (app t, J = 10.0 Hz, 1 H), 0.96 (s,

= 166.7, 163.6, 154.1, 141.4, 136.2, 135.58, 135.55, 133.3, 133.2,

129.9, 129.8, 129.3, 127.9, 127.8, 126.4, 116.8, 102.6, 81.9, 77.4,

9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 173.1, 160.4, 154.1,

145.7, 135.6, 133.3, 129.81, 129.77, 129.3, 127.9, 127.8, 126.4, 82.0,

77.3, 76.9, 64.6, 57.7, 53.0, 51.9, 50.0, 37.1, 33.2, 26.8, 19.3 ppm.

76.9, 64.7, 53.2, 51.8, 50.2, 26.8, 19.3 ppm. IR (neat): ν = 3300,

˜

3052, 2930, 1717, 1645, 1622, 1489, 1105 cm^–1. HRMS (ESI⁺):

calcd. for C₄₈H₅₀N₄O₅Si [M + Na] 813.3448; found 813.3449.

IR (KBr): ν = 3401, 2951, 1732, 1667, 1613, 1545, 1493, 1105 cm^–1.

˜

HRMS (ESI⁺): calcd. for C₄₈H₅₁N₄O₅SiI [M + Na] 941.2571;

found 941.2571.

Aza-Michael Addition Product 10a: Acrylonitrile (160 μL,

2.4 mmol), KOAc (74 mg, 0.75 mmol), and nBu₄NBr (106 mg,

0.33 mmol) were added under Ar to a stirred solution of 3 (250 mg,

0.3 mmol) in dry DMF (2.5 mL). The resulting mixture was stirred

and heated at 80 °C for 3 h. The reaction mixture was concentrated

in vacuo and the residue was dissolved in EtOAc (75 mL). The

organic phase was washed with water and brine and dried with

anhydrous Na₂SO₄. The solvent was removed under reduced pres-

sure, and the solid residue was purified by flash column chromatog-

raphy on silica gel (MeOH/CH₂Cl₂1–2%) to give the product 10

as a colorless foamy solid (250 mg, 94%). ¹H NMR (500 MHz,

CDCl₃): δ = 7.58–7.27 (comp, 23 H), 7.19–7.16 (m, 3 H), 6.12 (dd,

J = 9.2, 1.8 Hz, 1 H), 5.83 (t, J = 6.0 Hz, 1 H), 4.27–4.25 (m, 1 H),

3.75–3.66 (m, 3 H), 3.59 (dd, J = 10.8, 5.8 Hz, 1 H), 3.52 (d, J =

11.0 Hz, 1 H), 3.24 (d, J = 12.0 Hz, 1 H), 2.74 (t, J = 6.2 Hz, 2 H),

1.49 (app t, J = 11.0 Hz, 1 H), 1.17 (dd, J = 11.0, 9.5 Hz, 1 H),

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-8-bromoadenosine (13):

Bromine (0.42 mL) was added to an aqueous Na₂HPO₄solution

(10% w/v, 50 mL) and the mixture was stirred vigorously for 15 min

until most of the bromine had dissolved. The decanted bromine

solution (30 mL) was then added dropwise to a stirred solution of

12 (1.4 g, 1.9 mmol) in dioxane (40 mL) at 15 °C. The resulting

mixture was then stirred overnight at room temperature. The mix-

ture was cooled again (ice bath), and aqueous Na₂SO₃(25 mL,

1.5 m) was added dropwise. The reaction mixture was extracted

with EtOAc (2ϫ 100 mL). The combined organic layers were

washed with brine and dried with anhydrous Na₂SO₄. The solvent

was removed under reduced pressure, and the solid residue was

purified by flash column chromatography on silica gel (acetone/

CH₂Cl₂5–7%) to give the product 13 as a colorless foamy solid

(908 mg, conv. 59%; yield 71%, based on recovered starting mate-

0.96 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 160.8, 153.8, rial) together with unreacted 12 (236 mg). ¹H NMR (500 MHz,

146.4, 135.6, 133.3, 129.9, 129.8, 129.3, 127.9, 127.85, 127.82, CDCl₃): δ = 8.21 (s, 1 H), 7.56–7.25 (comp, 22 H), 7.20–7.17 (m,

126.5, 118.1, 82.2, 77.5, 76.9, 64.6, 56.8, 53.1, 50.0, 38.0, 26.9, 19.3, 3 H), 6.32 (dd, J = 10.2, 2.2 Hz, 1 H), 5.62 (br. s, 2 H), 4.31–4.28

1282

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Eur. J. Org. Chem. 2013, 1271–1286

Nucleobase-Functionalized Modified Nucleoside Monomers

(m, 1 H), 3.75 (dd, J = 10.8, 4.8 Hz, 1 H), 3.58 (dd, J = 10.5,

6.0 Hz, 1 H), 3.29 (d, J = 12.0 Hz, 1 H), 3.16 (d, J = 11.5 Hz, 1

H), 2.81 (app t, J = 10.8 Hz, 1 H), 1.62 (app t, J = 11.2 Hz, 1 H),

135.59, 135.56, 133.6, 133.5, 133.3, 129.74, 129.7, 129.4, 127.9,

127.73, 127.7, 126.5, 119.2, 100.8, 94.4, 81.9, 77.8, 76.9, 64.6, 50.6,

50.5, 26.9, 19.3, 7.6, 4.1 ppm. IR (neat): ν = 3315, 3183, 2957, 2874,

˜

0.95 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 154.4, 153.0, 2166, 1643, 1113 cm^–1. HRMS (ESI⁺): calcd. for C₅₃H₆₀N₆O₂Si₂

151.3, 135.61, 135.59, 133.4, 133.3, 129.74, 129.68, 129.3, 127.9, [M + Na] 891.4214; found 891.4214.

127.7, 127.66, 126.5, 125.6, 119.8, 82.2, 77.6, 77.1, 64.6, 49.9, 26.9,

Morpholino-Modified

7Ј-O-TBDPS-N-trityl-8-(1-hydroxyprop-2-

19.3 ppm. IR (KBr): ν = 3391, 3320, 2930, 2857, 1634, 1597, 1449,

˜

ynyl)adenosine (14d): A colorless solid (yield 62%) was isolated by

flash column chromatography on silica gel (MeOH/CH₂Cl₂3–4%).

¹H NMR (500 MHz, CDCl₃): δ = 8.32 (s, 1 H), 7.56–7.18 (comp,

25 H), 6.40 (dd, J = 10.5, 2.5 Hz, 1 H), 6.39 (br. s, 2 H), 4.35–4.31

(m, 1 H), 4.03 (s, 2 H), 3.76 (dd, J = 10.5, 4.5 Hz, 1 H), 3.53 (dd,

J = 10.5, 6.5 Hz, 1 H), 3.37 (d, J = 11.5 Hz, 1 H), 3.19 (d, J =

11.5 Hz, 1 H), 2.71 (app t, J = 10.8 Hz, 1 H), 1.52 (app t, J =

11.0 Hz, 1 H), 0.94 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ

= 155.2, 154.0, 149.5, 135.63, 135.62, 133.4, 133.3, 132.9, 129.8,

129.7, 129.4, 127.9, 127.8, 127.7, 126.5, 118.6, 96.0, 80.3, 77.2, 77.1,

1113, 710 cm^–1. HRMS (ESI⁺): calcd. for C₄₅H₄₅N₆O₂SiBr [M +

Na] 831.2454; found 831.2426.

General Procedure for Sonogashira Coupling of Morpholino-Modi-

fied 7Ј-O-TBDPS-N-trityl-8-bromoadenosine (13): Compound 13

(121 mg, 0.15 mmol) in dry DMF (1.6 mL) was placed in an oven-

dried round-bottomed flask. The solution was purged with Ar for

5–10 min. Triethylamine (84 μL, 0.6 mmol), the terminal acetylene

(amount according to Table 6), Pd(PPh₃)₂Cl₂(3.2 mg, 3 mol-%),

and CuI (2.3 mg, 8 mol-%), were added under Ar to this stirred

solution. The resulting mixture was heated at 90 °C for 3.5–16 h

(depending on the alkyne, Table 6). The reaction mixture was con-

centrated in vacuo and the residue was dissolved in CHCl₃(60 mL).

The organic layer was washed with water and brine and dried with

anhydrous Na₂SO₄. The solvent was removed under reduced pres-

sure, and the solid residue was purified by flash column chromatog-

raphy on silica gel in acetone/CH₂Cl₂or MeOH/CH₂Cl₂.

75.1, 64.7, 50.4, 50.3, 50.2, 26.9, 19.3 ppm. IR (neat): ν = 3327,

˜

3181, 2930, 2857, 2231, 1649, 1111 cm^–1. HRMS (ESI⁺): calcd. for

C₄₈H₄₈N₆O₃Si [M + Na] 807.3455; found 807.3454.

7Ј-O-TBDPS-N-trityl Morpholino-Modified 8-(Hex-1-ynyl)aden-

osine (14e): An off-white foamy solid (yield 68%) was isolated by

flash column chromatography on silica gel (acetone/CH₂Cl₂4–5%).

¹H NMR (500 MHz, CDCl₃): δ = 8.30 (s, 1 H), 7.56–7.26 (comp,

22 H), 7.19–7.16 (m, 3 H), 6.40 (dd, J = 10.0, 2.5 Hz, 1 H), 5.89

(br. s, 2 H), 4.36–4.34 (m, 1 H), 3.78 (dd, J = 10.5, 4.5 Hz, 1 H),

3.50 (dd, J = 10.0, 7.0 Hz, 1 H), 3.40 (d, J = 11.5 Hz, 1 H), 3.16

(d, J = 11.0 Hz, 1 H), 2.75 (app t, J = 10.8 Hz, 1 H), 2.10–2.05 (m,

2 H), 1.51 (app t, J = 11.0 Hz, 1 H), 1.34–1.26 (comp, 4 H), 0.95

(s, 9 H), 0.85–0.82 (m, 3 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ

= 155.0, 153.6, 149.6, 135.6, 134.2, 133.5, 133.3, 129.8, 129.7, 129.4,

127.9, 127.74, 127.71, 126.5, 118.9, 97.9, 80.6, 77.3, 77.0, 71.1, 64.7,

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-8-(phenylethynyl)aden-

osine (14a): An off-white foamy solid (yield 78%) was isolated by

flash column chromatography on silica gel (acetone/CH₂Cl₂5–6%).

¹H NMR (500 MHz, CDCl₃): δ = 8.35 (s, 1 H), 7.54–7.07 (comp,

30 H), 6.49 (dd, J = 10.5, 2.5 Hz, 1 H), 6.01 (br. s, 2 H), 4.40–4.38

(m, 1 H), 3.78 (dd, J = 10.0, 5.0 Hz, 1 H), 3.51 (dd, J = 10.2,

7.2 Hz, 1 H), 3.42 (d, J = 12.0 Hz, 1 H), 3.24 (d, J = 11.5 Hz, 1

H), 2.76 (app t, J = 10.8 Hz, 1 H), 1.56 (app t, J = 11.0 Hz, 1 H),

0.93 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 155.2, 153.9, 50.3, 29.8, 26.9, 22.1, 19.3, 18.9, 13.6 ppm. IR (neat): ν = 3314,

149.7, 135.6, 133.6, 133.5, 133.3, 132.0, 129.8, 129.7, 129.4, 128.5,

127.9, 127.7, 126.5, 120.8, 119.3, 95.1, 80.6, 79.3, 77.4, 77.1, 64.8,

˜

3165, 2930, 2859, 2239, 1647, 1597, 1449, 1113 cm^–1. HRMS

(ESI⁺): calcd. for C₅₁H₅₄N₆O₂Si [M + Na] 833.3975; found

833.3976.

50.8, 50.6, 26.9, 19.3 ppm. IR (neat): ν = 3314, 3165, 2928, 2857,

˜

2222, 1649, 1597, 1329, 1111 cm^–1. HRMS (ESI⁺): calcd. for

C₅₃H₅₀N₆O₂Si [M + Na] 853.3662; found 853.3663.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-8-(N-trifluoroacetyl-1-

aminoprop-2-ynyl)adenosine (14f): An off-white foamy solid (yield

63%) was isolated by flash column chromatography on silica gel

(acetone/CH₂Cl₂5–7%). ¹H NMR (500 MHz, CDCl₃): δ = 8.35 (s,

1 H), 7.56–7.26 (comp, 22 H), 7.18 (m, 3 H), 6.72 (s, 1 H), 6.52

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-8-(4-cyanophenylethyn-

yl)adenosine (14b): An off-white foamy solid (yield 74%) was iso-

lated by flash column chromatography on silica gel (acetone/

CH₂Cl₂5–6%). ¹H NMR (500 MHz, CDCl₃): δ = 8.42 (s, 1 H), (dd, J = 10.0, 2.0 Hz, 1 H), 5.64 (br. s, 2 H), 4.30–4.28 (m, 1 H),

7.56–7.10 (comp, 27 H), 7.05 (d, J = 8.5 Hz, 2 H), 6.53 (dd, J =

4.20 (br. s, 2 H), 3.72 (m, 2 H), 3.30 (d, J = 11.5 Hz, 1 H), 3.25 (d,

10.0, 2.5 Hz, 1 H), 5.93 (br. s, 2 H), 4.44–4.40 (m, 1 H), 3.78 (dd, J = 12.0 Hz, 1 H), 1.81 (app t, J = 11.0 Hz, 1 H), 1.70 (app t, J =

J = 10.5, 5.0 Hz, 1 H), 3.51 (dd, J = 10.5, 6.5 Hz, 1 H), 3.45 (d, J =

11.5 Hz, 1 H), 3.30 (d, J = 11.0 Hz, 1 H), 2.67 (app t, J = 10.8 Hz, 1

11.2 Hz, 1 H), 0.94 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ

2

= 154.9, 153.1, 150.6, 150.22 (q, J_C,F= 44.0 Hz), 150.2, 146.0,

H), 1.54 (app t, J = 11.0 Hz, 1 H), 0.93 (s, 9 H) ppm. ¹³C NMR 135.6, 135.5, 133.3, 133.0, 130.0, 129.9, 129.3, 128.0, 127.9, 127.8,

1

(125 MHz, CDCl₃): δ = 155.3, 154.5, 149.7, 135.6, 135.3, 133.4, 126.7, 125.9, 118.5, 116.5 (q, J_C,F= 271.6 Hz), 81.2, 77.6, 77.1,

133.2, 132.4, 132.2, 132.1, 129.8, 129.4, 127.9, 127.8, 126.6, 125.5,

119.4, 118.2, 112.9, 92.4, 83.3, 80.3, 77.4, 77.1, 64.9, 51.1, 50.5,

64.7, 52.4, 49.9, 26.8, 26.6, 19.3 ppm. IR (neat): ν = 3314, 3161,

˜

2930, 2857, 2242, 1717, 1647, 1207, 1153, 1111 cm^–1. HRMS

(ESI⁺): calcd. for C₅₀H₄₈N₇O₃F₃Si [M + Na] 902.3438; found

26.9, 19.3 ppm. IR (neat): ν = 3314, 3161, 2928, 2857, 2228, 1653,

˜

1603, 1489, 1109 cm^–1. HRMS (ESI⁺): calcd. for C₅₄H₄₉N₇O₂Si [M 902.3438.

+ Na] 878.3615; found 878.3616.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-8-(2-pyridylethynyl)-

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-8-(triethylsilylethynyl)- adenosine (14g): An off-white foamy solid (yield 65%) was isolated

adenosine (14c): An off-white foamy solid (yield 67%) was isolated

by flash column chromatography on silica gel (acetone/CH₂Cl₂4–

5%). ¹H NMR (500 MHz, CDCl₃): δ = 8.26 (s, 1 H), 7.56–6.16

(comp, 25 H), 6.44 (dd, J = 10.0, 2.0 Hz, 1 H), 5.92 (br. s, 2 H),

4.36–4.34 (m, 1 H), 3.80 (dd, J = 10.2, 4.8 Hz, 1 H), 3.53 (dd, J =

by flash column chromatography on silica gel (acetone/CH₂Cl₂6–

7%). H NMR (500 MHz, CDCl₃): δ = 8.63 (d, J = 4.5 Hz, 1 H),

8.36 (s, 1 H), 7.56–7.06 (comp, 27 H), 6.97 (d, J = 7.5 Hz, 1 H),

6.53 (br. s, 2 H), 6.50 (dd, J = 9.8, 2.2 Hz, 1 H), 4.41–4.39 (m, 1

H), 3.83 (dd, J = 10.0, 5.0 Hz, 1 H), 3.60 (dd, J = 10.0, 7.0 Hz, 1

1

10.0, 8.0 Hz, 1 H), 3.41 (d, J = 11.5 Hz, 1 H), 3.18 (d, J = 11.0 Hz, H), 3.42 (d, J = 12.0 Hz, 1 H), 3.26 (d, J = 11.5 Hz, 1 H), 2.76

1 H), 2.75 (app t, J = 10.8 Hz, 1 H), 1.56 (app t, J = 11.0 Hz, 1 (app t, J = 10.8 Hz, 1 H), 1.63 (app t, J = 11.0 Hz, 1 H), 0.94 (s,

H), 1.00 (t, J = 7.8 Hz, 9 H), 0.96 (s, 9 H), 0.61 (q, J = 8.0 Hz, 6 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 155.6, 154.4, 150.5,

H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 155.3, 154.0, 149.5,

149.6, 141.4, 136.1, 135.6, 133.6, 133.3, 132.6, 129.7, 129.6, 129.4,

Eur. J. Org. Chem. 2013, 1271–1286

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1283

B. Nandi, S. Pattanayak, S. Paul, S. Sinha

FULL PAPER

127.9, 127.73, 127.69, 127.4, 126.4, 123.9, 119.6, 93.7, 80.7, 78.6.

1

129.3, 129.2, 127.85, 127.8, 126.5, 120.5 (q, J_C,F= 258.4 Hz),

77.3, 77.1, 64.8, 50.9, 50.4, 26.9, 19.3 ppm. IR (neat): ν = 3316,

120.3, 119.1, 80.9, 77.4, 77.0, 64.8, 49.7, 26.9, 19.3 ppm. IR (neat):

˜

3175, 2930, 2857, 2228, 1651, 1595, 1574, 1427, 1113 cm^–1. HRMS

(ESI⁺): calcd. for C₅₂H₄₉N₇O₂Si [M + Na] 854.3615; found

854.3615.

ν = 3318, 3169, 2930, 2857, 1645, 1599, 1258, 1113 cm^–1. HRMS

˜

(ESI⁺): calcd. for C₅₂H₄₉N₆O₃F₃Si [M + Na] 913.3485; found

913.3486.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-8-(4-fluorophenyl)ad-

enosine (15d): An off-white foamy solid (yield 79%) was isolated

by flash column chromatography on silica gel (acetone/CH₂Cl₂5–

6%). ¹H NMR (500 MHz, CDCl₃): δ = 8.38 (s, 1 H), 7.60–7.14

(comp, 27 H), 6.88 (app t, J = 8.5 Hz, 2 H), 6.30 (dd, J = 10.2,

2.2 Hz, 1 H), 6.07 (br. s, 2 H), 4.32–4.28 (m, 1 H), 3.79 (dd, J =

10.5, 4.5 Hz, 1 H), 3.57 (dd, J = 10.8, 6.2 Hz, 1 H), 3.22 (d, J =

11.5 Hz, 1 H), 2.89 (d, J = 11.5 Hz, 1 H), 2.25 (app t, J = 11.0 Hz,

1 H), 1.36 (app t, J = 11.0 Hz, 1 H), 0.97 (s, 9 H) ppm. ¹³C NMR

(125 MHz, CDCl₃): δ = 163.9 (¹J_C,F= 251.5 Hz), 155.1, 152.6,

151.3, 150.9, 135.6, 133.3, 133.2, 132.1 (³J_C,F= 7.5 Hz), 129.9,

129.8, 129.2, 127.9, 127.8, 126.6 (⁴J_C,F= 3.4 Hz), 126.4, 118.9,

115.6 (²J_C,F= 21.4 Hz), 80.9, 77.3, 77.0, 64.7, 49.7, 49.5, 26.9,

General Procedure for Suzuki Coupling of Morpholino-Modified 7Ј-

O-TBDPS-N-trityl-8-bromoadenosine (13): K₃PO₄(3 m in H₂O,

150 μL, 0.45 mmol), the arylboronic acid (0.33 mmol), and

Pd(dppf)Cl₂·CH₂Cl₂(9 mg, 0.011 mmol) were added under Ar to

a stirred solution of 13 (121 mg, 0.15 mmol) in dry dioxane

(2.5 mL). The resulting mixture was heated at 90 °C for 11–14 h

(depending on the boronic acid, Table 7). The reaction mixture was

concentrated in vacuo and the residue was dissolved in EtOAc

(60 mL). The organic phase was washed with water and brine and

dried with anhydrous Na₂SO₄. The solvent was removed under re-

duced pressure, and the solid residue was purified by flash column

chromatography on silica gel in acetone/CH₂Cl₂to give a colorless

foamy solid product.

19.3 ppm. IR (neat): ν = 3440, 3019, 2931, 1636, 1215, 758 cm^–1.

˜

Morpholino-Modified

7Ј-O-TBDPS-N-trityl-8-(phenyl)adenosine

HRMS (ESI⁺): calcd. for C₅₁H₄₉N₆O₂FSi [M + Na] 847.3568;

found 847.3566.

(15a): An off-white foamy solid (yield 72%) was isolated by flash

1

column chromatography on silica gel (acetone/CH₂Cl₂5–6%). H

7Ј-O-TBDPS-N-trityl Morpholino-Modified 8-(1-Naphthyl)aden-

osine (15e): An off-white foamy solid (yield 84%) was isolated by

flash column chromatography on silica gel (acetone/CH₂Cl₂5–6%).

¹H NMR (500 MHz, CDCl₃, mixture of rotamers): δ = 8.31 (s, 1

H), 7.90–7.87 (m, 2 H), 7.52–7.10 (comp, 30 H), 6.02 (br. s, 1 H),

5.84 (br. s, 2 H), 4.00 (br. s, 1 H), 3.58 (br. s, 1 H), 3.19 (br. s, 1

H), 3.10 (d, J = 11.5 Hz, 1 H), 2.96 (d, J = 10.5 Hz, 1 H), 2.14 (br.

s, 1 H), 1.06 (app t, J = 11.8 Hz, 1 H), 0.91(s, 9 H) ppm. ¹³C NMR

(125 MHz, CDCl₃): δ = 155.3, 153.0, 151.0, 150.0, 135.6, 133.45,

133.0, 132.5, 130.7, 129.8, 129.7, 129.4, 129.2, 128.4, 127.7, 127.2,

126.5, 126.3, 125.5, 124.5, 119.3, 81.5, 77.0, 76.8, 64.4, 50.1, 50.0,

NMR (500 MHz, CDCl₃): δ = 8.26 (s, 1 H), 7.63 (d, J = 7.5 Hz, 2

H), 7.57 (d, J = 7.0 Hz, 2 H), 7.52 (d, J = 7.0 Hz, 2 H), 7.44–7.19

(comp, 21 H), 7.15–7.12 (m, 3 H), 6.21 (dd, J = 10.0, 1.5 Hz, 1 H),

5.91 (br. s, 2 H), 4.27–4.25 (m, 1 H), 3.78 (dd, J = 10.5, 5.0 Hz, 1

H), 3.56 (dd, J = 10.5, 6.5 Hz, 1 H), 3.22 (d, J = 12.0 Hz, 1 H),

2.97 (d, J = 11.0 Hz, 1 H), 2.58 (app t, J = 10.8 Hz, 1 H), 1.40

(app t, J = 11.0 Hz, 1 H), 0.97 (s, 9 H) ppm. ¹³C NMR (125 MHz,

CDCl₃): δ = 155.3, 152.8, 151.8, 151.4, 135.6, 133.4, 133.3, 130.44,

130.37, 129.9, 129.8, 129.7, 129.3, 128.5, 127.8, 127.7, 126.4, 119.2,

81.6, 77.3, 77.0, 64.8, 49.8, 49.7, 26.9, 19.3 ppm. IR (neat): ν =

˜

3314, 3171, 2930, 2857, 1647, 1472, 1111 cm^–1. HRMS (ESI⁺):

calcd. for C₅₁H₅₀N₆O₂Si [M + Na] 829.3662; found 829.3663.

26.9, 19.3 ppm. IR (neat): ν = 3312, 3167, 2928, 2856, 1645,

˜

1113 cm^–1. HRMS (ESI⁺): calcd. for C₅₅H₅₂N₆O₂Si [M + Na]

879.3819; found 879.3768.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-8-(4-methoxyphenyl)-

adenosine (15b): An off-white foamy solid (yield 76%) was isolated

by flash column chromatography on silica gel (acetone/CH₂Cl₂5–

Morpholino-Modified

N²-Isobutyryl-N-trityl-8-bromoguanosine

(19): Bromine (0.21 mL) was added to an aqueous Na₂HPO₄solu-

tion (10% w/v, 25 mL) and the mixture was stirred vigorously for

15 min until most of the bromine had dissolved. The decanted

bromine solution (10 mL) was then added dropwise at 15 °C to a

stirred solution of 18 (410 mg, 0.71 mmol) in dioxane (13 mL). The

reaction mixture was then stirred for 6 h at room temperature and

became colorless. The reaction mixture was extracted with CHCl₃

(2ϫ 60 mL). The combined organic layers were washed with brine

and dried with anhydrous Na₂SO₄. The solvent was removed under

reduced pressure, and the solid residue was purified by flash col-

umn chromatography on silica gel (MeOH/CH₂Cl₂2–3%) to give

the product 19 as a colorless solid (331 mg, conv. 71%, yield 82%

based on recovered starting material) together with unreacted 18

(58 mg), m.p. 188–190 °C (dec.). ¹H NMR (500 MHz, [D₆]DMSO):

δ = 12.12 (br. s, 1 H), 11.62 (br. s, 1 H), 7.44–7.32 (comp, 12 H),

7.20 (br. s, 3 H), 6.26 (d, J = 10.0 Hz, 1 H), 4.83 (t, J = 5.2 Hz, 1

H), 4.17 (br. s, 1 H), 3.46–3.44 (m, 1 H), 3.31 (dd, J = 11.0, 5.5 Hz,

1 H), 3.16 (d, J = 11.5 Hz, 1 H), 3.10 (d, J = 11.0 Hz, 1 H), 2.84

(sept, J = 6.8 Hz, 1 H), 2.44 (app t, J = 10.5 Hz, 1 H), 1.42 (app

t, J = 11.0 Hz, 1 H), 1.14 (d, J = 6.5 Hz, 6 H) ppm. ¹³C NMR

(125 MHz, [D₆]DMSO): δ = 180.2, 153.5, 149.6, 148.3, 128.8,

127.9, 126.4, 121.1, 120.3, 81.2, 77.5, 76.4, 61.8, 49.7, 49.4, 34.7,

1

6%). H NMR (500 MHz, CDCl₃): δ = 8.28 (s, 1 H), 7.59 (d, J =

9.0 Hz, 2 H), 7.58 (d, J = 8.5 Hz, 2 H), 7.54 (d, J = 7.5 Hz, 2 H),

7.40–7.18 (comp, 18 H), 7.14–7.11 (comp, 3 H), 6.79 (d, J = 8.5 Hz,

2 H), 6.24 (d, J = 10.0 Hz, 1 H), 5.88 (br. s, 2 H), 4.30–4.28 (m, 1

H), 3.86 (s, 3 H), 3.80 (dd, J = 10.2, 5.2 Hz, 1 H), 3.61 (dd, J =

10.5, 6.5 Hz, 1 H), 3.21 (d, J = 11.5 Hz, 1 H), 2.91 (d, J = 11.0 Hz,

1 H), 2.53 (app t, J = 11.0 Hz, 1 H), 1.43 (app t, J = 11.0 Hz, 1

H), 0.98 (s, 9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 161.2,

155.1, 152.5, 151.8, 151.4, 135.64, 135.61, 133.4, 133.3, 131.4,

129.8, 129.7, 129.3, 127.8, 127.7, 126.4, 122.6, 119.0, 113.9, 81.2,

77.4, 77.0, 64.8, 55.4, 49.7, 49.3, 26.9, 19.3 ppm. IR (neat): ν =

˜

3318, 3167, 2930, 2857, 1643, 1605, 1487, 1254, 1113 cm^–1. HRMS

(ESI⁺): calcd. for C₅₂H₅₂N₆O₃Si [M + Na] 859.3768; found

859.3768.

Morpholino-Modified 7Ј-O-TBDPS-N-trityl-8-(4-trifluoromethoxy-

phenyl)adenosine (15c): An off-white foamy solid (yield 77%) was

isolated by flash column chromatography on silica gel (acetone/

CH₂Cl₂5–6%). ¹H NMR (500 MHz, CDCl₃): δ = 8.35 (s, 1 H),

7.67 (d, J = 8.5 Hz, 2 H), 7.58 (d, J = 7.0 Hz, 2 H), 7.53 (d, J =

7.5 Hz, 2 H), 7.41–7.14 (comp, 21 H), 7.04 (d, J = 8.5 Hz, 2 H),

6.33 (dd, J = 10.8, 2.2 Hz, 1 H), 5.93 (br. s, 2 H), 4.33–4.29 (m, 1

H), 3.79 (dd, J = 10.5, 5.0 Hz, 1 H), 3.58 (dd, J = 10.2, 6.2 Hz, 1

H), 3.22 (d, J = 12.0 Hz, 1 H), 2.92 (d, J = 12.0 Hz, 1 H), 2.29

(app t, J = 11.0 Hz, 1 H), 1.35 (app t, J = 11.2 Hz, 1 H), 0.98 (s,

9 H) ppm. ¹³C NMR (125 MHz, CDCl₃): δ = 155.4, 153.0, 151.5,

18.83, 18.77 ppm. IR (neat): ν = 3376, 3160, 2930, 1639, 1607,

˜

1559, 1449 cm^–1. HRMS (ESI⁺): calcd. for C₃₃H₃₃N₆O₄Br⁸¹[M +

Na] 681.1624; found 681.1631.

Morpholino-Modified

N²-Isobutyryl-N-trityl-8-(phenylethynyl)-

150.6, 150.4, 135.64, 135.62, 133.3, 133.2, 131.8, 129.9, 129.86, guanosine (20): Compound 19 (105 mg, 0.16 mmol) in dry DMF

1284

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Eur. J. Org. Chem. 2013, 1271–1286

Nucleobase-Functionalized Modified Nucleoside Monomers

(1.7 mL) was placed in an oven-dried round-bottomed flask. The

solution was purged with Ar for 5–10 min. Triethylamine (90 μL,

0.64 mmol), phenylacetylene (44 μL, 0.4 mmol), Pd(PPh₃)₂Cl₂

(4.5 mg, 4 mol-%), and CuI (2.4 mg, 8 mol-%) were added under

Ar to this stirred solution. The resulting mixture was heated at

90 °C overnight. The reaction mixture was concentrated in vacuo

and the residue was dissolved in CHCl₃(60 mL). The organic layers

were washed with water and brine and dried with anhydrous

Na₂SO₄. The solvent was removed under reduced pressure, and the

solid residue was purified by flash column chromatography on sil-

ica gel (MeOH/CH₂Cl₂2–3%; note: R_fof 20 is the same as that of

the staring material 19 but product 20 is short-wavelength UV

active) to give the product 20 as a colorless solid (96 mg, 88%). ¹H

NMR (500 MHz, [D₆]DMSO): δ = 12.16 (s, 1 H), 11.80 (s, 1 H),

7.49–7.25 (comp, 15 H), 7.10–7.08 (m, 5 H), 6.26 (d, J = 10.0 Hz,

1 H), 4.82 (t, J = 5.5 Hz, 1 H), 4.18–4.16 (m, 1 H), 3.41–3.38 (m,

1 H), 3.24–3.13 (m, 3 H), 2.85 (sept, J = 6.8 Hz, 1 H), 2.57 (app t,

J = 10.8 Hz, 1 H), 1.48 (app t, J = 11.2 Hz, 1 H), 1.15 (d, J =

6.5 Hz, 6 H) ppm. ¹³C NMR (125 MHz, [D₆]DMSO): δ = 180.8,

154.6, 149.6, 148.6, 131.7, 130.6, 130.3, 129.2, 128.3, 126.9, 120.6,

120.3, 93.5, 80.2, 80.1, 77.6, 76.9, 62.5, 50.7, 50.2, 35.3, 19.4,

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Acknowledgments

S. S. thanks the Council of Scientific and Industrial Research

(CSIR), New Delhi. India for financial support (grant number

02(0012)/11/EMR-II). B. N., S. P., and S. P. are thankful to CSIR

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Received: October 18, 2012

Published Online: January 18, 2013

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Synthesis of nucleobase-functionalized morpholino-modified nucleoside monomers through palladium-catalyzed cross-coupling reactions

DOI: 10.1002/ejoc.201201384

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