N-3-alkylation of uracil and derivatives via N-1-BOC protection

Article abstract of DOI:10.1081/SCC-100108223

An easy and efficient synthesis of 3-alkyluracils is described. Thus, BOC-protection at N-1 of uracil permits selective alkylation at N-3. This protecting group can be removed under very mild conditions.

Full text of DOI:10.1081/SCC-100108223

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N-3-ALKYLATION OF URACIL AND DERIVATIVES VIA
N-1-BOC PROTECTION
Saul Jaime-Figueroa a , Alejandro Zamilpa a , Angel Guzmán a & David J. Morgans Jr. a
a Roche Bioscience, 3401 Hillview Ave., Palo Alto, CA, 94304, U.S.A.
Version of record first published: 09 Nov 2006.
To cite this article: Saul Jaime-Figueroa , Alejandro Zamilpa , Angel Guzmán & David J. Morgans Jr. (2001): N-3-
ALKYLATION OF URACIL AND DERIVATIVES VIA N-1-BOC PROTECTION, Synthetic Communications: An International Journal
for Rapid Communication of Synthetic Organic Chemistry, 31:24, 3739-3746
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SYNTHETIC COMMUNICATIONS, 31(24), 3739–3746 (2001)
N-3-ALKYLATION OF URACIL
AND DERIVATIVES VIA
N-1-BOC PROTECTION
Saul Jaime-Figueroa,* Alejandro Zamilpa,
Angel Guzman,and David J. Morgans,Jr.
Roche Bioscience, 3401 Hillview Ave., Palo Alto,
CA 94304, USA
ABSTRACT
An easy and efficient synthesis of3-alkyluracils is described.
Thus, BOC-protection at N-1 ofuracil permits selective alky-
lation at N-3. This protecting group can be removed under
very mild conditions.
1
In one ofour research programs we required a versatile method to
prepare substantial quantities ofvarious 3-alkyluracils. One approach of r
the synthesis ofsuch compounds is a three-step sequence involving protec-
tion ofthe N-1 position, alkylation at N-3, and then deprotection. The
protecting groups which have been utilized for this purpose include
SEM,2 acyl,3 benzyl,4 benzyloxymethyl,5 and tetrahydropyranyl.6 However,
most ofthese protecting groups have problems associated with either their
introduction or removal.2–8 We report the use ofdi- t-butyldicarbonate9
(BOC)2O, as an easy and inexpensive way to protect the N-1 position in
*Corresponding author. E-mail: saul.jaime@roche.com
3739
Copyright & 2001 by Marcel Dekker, Inc.
www.dekker.com

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JAIME-FIGUEROA ET AL.
uracil derivatives. This regioselective protection permits the alkylation ofthe
nitrogen at N-3 without any complications.
Reaction ofuracils 1a–i with di-t-butyldicarbonate in acetonitrile con-
taining a catalytic amount of4-DMAP, gave the protected 1- N-BOC-uracils
2a–i in good yields, independent ofthe nature ofthe 5-substituent (Table 1).
Only 5-nitrouracil 1j failed to react under these conditions. The regioche-
mistry ofthese derivatives was determined using HETCOR-NMR spectro-
scopy. A correlation between the vinylmethine at H-6 and the three carbonyl
carbons at C-2, C-4 and ofthe BOC substituent was demonstrated.
The N-1 protected uracils 2 were deprotonated with NaH in DMF and
then reacted with benzyl bromide, 1-bromo-2-methylpropane or allyl bro-
mide to produce the 3-alkylated derivatives 3 in moderate to good yield;
some deprotection to give 4 was also observed (Table 2). It is noteworthy
that the protection and alkylation conversion of 1 to 3, may be done in one
pot (Table 3).
The N-1-BOC-3-alkyluracils 3 were deprotected in very high yield to
the corresponding 3-alkylated uracils 4 by reaction with methanolic K2CO3
solution at room temperature (Table 4).
Table 1. Preparation of N-1-BOC-Uracils 2
Substrate
X
Y
Product
Yield (%)
1a
1b
1c
1d
1e
1f
-H
-Me
-Br
-OMe
-CF3
-n-Pr
-Me
-F
-COOMe
-NO2
-H
-H
-H
-H
-H
-H
-Me
-H
-H
-H
2a
2b
2c
2d
2e
2f
70
92
87
64
93
79
59
1g
1h
1i
2g
2h
2i
68
80
1j
2j
No reaction

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3741
Table 2. Alkylation of N-1-BOC-Uracils
X
Yield (%)
Yield (%)
R
Time (h)
2a
2b
2c
-H
3a
3b*
3c
82
14
54
4a
4b
4c
5
50
30
-Bn
-i-Bu
-Allyl
0.5
24
2
-Me
-Br
3d
3e*
3f
84
54
74
4d
4e
4f
5
22
10
-Bn
-i-Bu
-Allyl
0.5
24
2
3g
3h
34
40
4g
4h
30
43
-Bn
-Allyl
12
2
2d
2e
-OMe
3i
3j
60
69
4i
4j
18
15
-Allyl
-Allyl
2
2
-n-Pr
*The reaction temperature was 50ꢀC.
Table 3. One Pot N-3-Alkylation ofUracils
Substrate
X
R
Product
Yield* (%)
1a
1b
1c
-H
-Me
-Br
-Bn
-Bn
-Bn
3a
3d
3g
67
73
52
*In each ofthese cases small amounts ofthe deprotected product was obtained as a
minor component.

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JAIME-FIGUEROA ET AL.
Table 4. Deprotection of N-1-BOC-N-3-Alkyluracils
Substrate
X
R
Product*
Yield (%)
3a
3b
3d
3e
3g
-H
-H
-Me
-Me
-Br
-Bn
-i-Bu
-Bn
-i-Bu
-Bn
4a
4b
4d
4e
4g
97
92
94
90
98
*All ofthese products were compared with authentic samples rfom our previous
work.2
In summary, we have developed a practical, fast and economical
method for the preparation of 3-alkyluracils by protecting the N-1 nitrogen
with a BOC substituent, which may be easily adapted for kilogram scale
preparations.
EXPERIMENTAL
Typical Procedure for the Preparation of N-1-BOC-Uracils
1-t-Butoxycarbonylthymine1a (2b). To a solution of( t-BOC)2O (8.63 g,
39.6 mmol) and thymine (5 g, 39.6 mmol) in MeCN (200 mL) was added
4-DMAP (48 mg, 0.39 mmol), and the reaction mixture was stirred for 4 h
at room temp. The solvent was removed under vacuum, and the residue was
purified by flash column chromatography (silica gel, hexane–AcOEt, 7:3)
to give 2b (8.26 g) in 92% ofyield as a solid. Mp ¼ 131–132ꢀC dec. (CH2Cl2–
1
hexane); H NMR (DMSO-d6) d 1.52 (s, 9H, -t-Bu), 1.80 (s, 3H, -Me), 7.76
(s, 1H, H-6), 11.44 (s, 1H, H-3); Anal. calc. for C10H14N2O4: C, 53.08; H,
6.23; N, 12.38. Found: C, 53.03; H, 6.18; N, 12.13.
2a: Mp 128–129ꢀC dec. (CH2Cl2–hexane); 1H NMR (DMSO-d6) d
1.52 (s, 9H, -t-Bu), 5.7 (d, 1H, H-5, J ¼ 8.3), 7.89 (s, 1H, H-6, J ¼ 8.3),

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3743
11.43 (broad s, 1H, H-3); Anal. calc. for C9H12N2O4: C, 50.93; H, 5.70; N,
13.20. Found: C, 51.29; H, 5.62; N, 13.13.
2c: Mp 123–124ꢀC dec. (CH2Cl2–hexane); 1H NMR (DMSO-d6) d 1.52
(s, 9H, -t-Bu), 8.24 (s, 1H, H-6), 11.92 (broad s, 1H, H-3); Anal. calc.
for C9H11N2BrO4: C, 37.13; H, 3.80; N, 9.62. Found: C, 37.21; H, 3.68;
N, 9.40.
2d: Mp 126ꢀC dec. (CH2Cl2–hexane); H NMR (DMSO-d6) d 1.52 (s,
1
9H, -t-Bu), 3.65 (s, 3H, -OMe), 7.34 (s, 1H, H-6), 11.60 (broad s, 1H, H-3);
Anal. calc. for C10H14N2O5: C, 49.58; H, 5.82; N, 11.56. Found: C, 49.84; H,
5.90; N, 11.21.
2e: Mp 109–110ꢀC dec. (CH2Cl2–hexane); 1H NMR (DMSO-d6) d 1.54
(s, 9H, -t-Bu), 8.30 (s, 1H, H-6), 11.95 (broad s, 1H, H-3); Anal. calc.
for C10H11N2F3O4: C, 42.87; H, 3.96; N, 10.00. Found: C, 43.20; H, 3.79;
N, 9.97.
2f: Mp 106–107ꢀC dec. (CH2Cl2–hexane); 1H NMR (DMSO-d6) d 0.87
(t, 3H, -Me), 1.40–1.56 (m, 2H, C-CH2-Me), 1.52 (s, 9H, -t-Bu), 2.20 (t, 2H,
-CH2-Et), 7.68 (s, 1H, H-6), 11.41 (s, 1H, H-3); Anal. calc. for C12H18N2O4:
C, 56.68; H, 7.13; N, 11.02. Found: C, 56.65; H, 7.26; N, 10.90.
2g: Mp 139–140ꢀC dec. (CH2Cl2–hexane); 1H NMR (DMSO-d6) d 1.49
(s, 9H, -t-Bu), 1.75 (s, 3H, -Me), 2.07 (s, 3H, -Me), 11.26 (broad s, 1H, H-3);
Anal. calc. for C11H16N2O4: C, 54.98; H, 6.71; N, 11.66. Found: C, 54.95; H,
6.64; N, 11.35.
2h: Mp 149–150ꢀC dec. (CH2Cl2–hexane); 1H NMR (DMSO-d6) d
1.53 (s, 9H, -t-Bu), 8.14 (d, 1H, H-6), 11.93 (broad s, 1H, H-3); Anal.
calc. for C9H11N2FO4: C, 46.95; H, 4.81; N, 12.17. Found: C, 46.67; H, 4.77;
N, 11.98.
2i: Mp 135–137ꢀC dec. (CH2Cl2–hexane); 1H NMR (DMSO-d6) d 1.53
(s, 9H, -t-Bu), 3.74 (s, 3H, -COOMe), 8.54 (s, 1H, H-6), 11.66 (s, 1H, H-3);
Anal. calc for C11H14N2O6: C, 48.88; H, 5.22; N, 10.36. Found: C, 49.06; H,
5.28; N, 10.21.
Typical Procedure for the Alkylation of N-1-BOC-Uracils
3-Benzyl-1-t-butoxycarbonylthymine (3d). To a suspension of60%
ofNaH (0.328 g, 8.22 mmol) in DMF was added 1.54 g (6.85 mmol) of
1-t-butoxycarbonylthymine 2b at 0ꢀC. The reaction mixture was stirred at
0ꢀC for 30 min then 1.4 g (8.22 mmol) of benzyl bromide was added into.
The reaction mixture was allowed to reach room temp. (30 min), poured
into cold water (200 mL), and the product was extracted with EtOAc
(3 ꢁ 100 mL). The organic extracts were washed with water (5 ꢁ 100 mL),
dried (Na2SO4) and evaporated to dryness. The residue was purified by flash

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3744
JAIME-FIGUEROA ET AL.
column chromatography (silica gel, hexane–EtOAc, 9:1). 1.8 g (84%) of
pure 3d was obtained as a solid; mp 109–110ꢀC (CH2Cl2–hexane);
1H NMR (DMSO-d6) d 1.53 (s, 9H, -t-Bu), 1.87 (s, 3H, -Me), 4.97 (s, 2H,
-Bn), 7.15–7.45 (m, 5H, -Ph), 7.87 (s, 1H, H-6); Anal. calc. for C17H20N2O4:
C, 64.53; H, 6.37; N, 8.85. Found: C, 64.27; H, 6.30; N, 8.72.
3a: Mp 108ꢀC (CH2Cl2–hexane); H NMR (DMSO-d6) d 1.52 (s, 9H,
1
-t-Bu), 4.96 (s, 2H, -Bn), 5.9 (d, 1H, H-5, J ¼ 8.3) 7.17–7.40 (m, 5H, -Ph),
7.98 (s, 1H, H-6, J ¼ 8.3); Anal. calc. for C16H18N2O4: C, 63.56; H, 6.00; N,
9.26. Found: C, 63.69; H, 6.04; N, 9.19.
3b: Mp 70–71ꢀC (CH2Cl2–hexane); H NMR (DMSO-d6) d 0.83 (d,
1
6H, i-Bu), 1.53 (s, 9H, -t-Bu), 1.99 (m, 1H, -CH(Me)2), 3.61 (d, 2H,
i-Pr-CH2-), 5.82 (d, 1H, H-5, J ¼ 8.3), 7.92 (d, 1H, H-6, J ¼ 8.3); Anal.
calc. for C33H20N2O4: C, 58.19; H, 7.51; N, 10.44. Found: C, 58.20; H, 7.74;
N, 10.23.
3c: Oil; 1H NMR (DMSO-d6) d 1.53 (s, 9H, -t-Bu), 4.36 (m, 2H, -allyl),
5.1 (m, 2H, vinyl), 5.71–5.90 (m, 1H, vinyl), 5.84 (d, 1H, H-5, J ¼ 8.3) 7.95
(d, 1H, H-6, J ¼ 8.3); Anal. calc. for C12H16N2O4: C, 57.12; H, 6.39; N,
11.10. Found: C, 57.40; H, 6.45; N, 11.12.
3e: Mp 81–82ꢀC (CH2Cl2–hexane); 1H NMR (DMSO-d6) d 0.82 (d, 6H,
-i-Bu), 1.53 (s, 9H, -t-Bu), 1.85 (s, 3H, -Me), 1.90–2.08 (m, 1H, -CH(Me)2),
3.63 (d, 2H, i-Pr-CH2-), 7.81 (s, 1H, H-6); Anal. calc. for C14H22N2O4: C,
59.55; H, 7.85; N, 9.92. Found: C, 59.70; H, 8.01; N, 9.67.
3f: Mp 55ꢀC (hexane); 1H NMR (DMSO-d6) d 1.53 (s, 9H, -t-Bu), 1.85
(s, 3H, -Me), 4.38 (m, 2H, -allyl), 5.03–5.13 (m, 2H, vinyl), 5.79–5.90 (m,
1H, vinyl), 8.84 (s, 1H, H-6); Anal. calc. for C33H18N2O4: C, 58.63; H, 6.81;
N, 10.52. Found: C, 58.79; H, 6.86; N, 10.15.
3g: Mp 115–116ꢀC (hexane); 1H NMR (DMSO-d6) d 1.53 (s, 9H, -t-Bu),
5.00 (s, 2H, -Bn), 7.15–7.40 (m, 5H, -Ph), 8.36 (s, 1H, H-6); Anal. calc.
for C16H17N2BrO4: C, 50.40; H, 4.49; N, 7.34. Found: C, 50.22; H, 4.43;
N, 7.17.
3h: Mp 86–88ꢀC (hexane); 1H NMR (DMSO-d6) d 1.54 (s, 9H, -t-Bu),
4.41 (d, 2H, -allyl), 5.15 (m, 2H, vinyl), 5.70–5.90 (m, 1H, vinyl), 8.33 (s, 1H,
H-6); Anal. calc. for C12H15N2BrO4.0.04 hex.; C, 43.98; H, 4.59; N, 8.38.
Found: C, 44.00; H, 4.59; N, 8.38.
3i: Oil; 1H NMR (DMSO-d6) d 1.54 (s, 9H, -t-Bu), 3.68 (s, 3H, -OMe)
4.38 (d, 2H, -allyl), 5.09 (m, 2H, vinyl), 5.70–5.89 (m, 1H, vinyl), 7.43 (s, 1H,
H-6); Anal. calc. for C33H18N2O5: C, 55.30; H, 6.42; N, 9.92. Found: C,
55.22; H, 6.63; N, 9.78.
1
3j: Oil; H NMR (DMSO-d6) d 0.87 (t, 3H, -Me), 1.40–1.60 (m, 2H,
Me-CH2-C), 1.53 (s, 9H, -t-Bu), 2.26 (t, 2H, -CH2-Et), 4.38 (d, 2H, -allyl),
5.12 (m, 2H, vinyl), 5.70–5.93 (m, 1H, vinyl), 7.76 (s, 1H, H-6); Anal. calc. for
C15H22N2O4: C, 61.20; H, 7.53; N, 9.52. Found: C, 61.42; H, 7.83; N, 9.45.

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3745
One Pot Procedure for the Preparation of
N-1-BOC-N-3-Alkyluracils
3-Benzyl-1-t-butoxycarbonylthymine (3d). a) To
a
solution of
(t-BOC)2O (2.18 g, 10 mmol) and thymine (1.26 g, 10 mmol) in MeCN
(100 mL) was added 4-DMAP (12 mg, 0.1 mmol) and the reaction mixture
was stirred for 3 h at room temperature. The solvent was removed under
vacuum and the residue was used in the next step.
b) The crude material from the previous step was diluted with DMF
(50 mL) and 0.480 g ofNaH (60%, 12 mmol) was added. The suspension
was stirred for 30 min at 0ꢀC, and then 2.05 g (12 mmol) ofbenzyl bromide
was added. The reaction was allowed to reach room temp. (30 min),
poured into cold water (100 mL). The product was extracted with EtOAc
(3 ꢁ 50 mL), and the organic extracts were washed with water (5 ꢁ 50 mL),
dried (Na2SO4) and evaporated to dryness. The residue was purified by flash
column chromatography (silica gel, hexane–EtOAc, 9:1) giving 2.3 g (73%)
ofthe pure product 3d as a solid; mp 109–110ꢀC (CH2Cl2–hexane).
Typical Procedure for the Removal of the BOC-Group in Uracils
3-Benzyluracil2,8 (4a). To a solution of590 mg (1.65 mmol) of1-BOC-
3-benzyluracil 3a in MeOH (30 mL) was added 114 mg (0.87 mmol) of
K2CO3 at room temperature. The reaction mixture was stirred for 2 h at
room temperature. The solvent was removed under vacuum. The residue
was diluted with CH2Cl2 (30 mL) and washed with an aqueous saturated
solution ofNH 4Cl (30 mL); the organic phase was dried (Na2SO4) and
evaporated to dryness. The crude material was crystallized from CH2Cl2–
hexane, to obtain 319 mg (96%) ofpure 4a as a solid; mp ¼ 177–178ꢀC
1
(CH2Cl2–hexane), Lit.9 mp 169–172; H NMR (DMSO-d6) d 4.94 (s, 2H,
-Bn), 5.63 (d, 1H, H-5, J ¼ 8.6) 7.15–7.35 (m, 5H, -Ph), 7.47 (s, 1H, H-6,
J ¼ 7.6); Anal. calc. for C11H10N2O4: C, 65.33; H, 4.98; N, 13.85. Found: C,
65.13; H, 4.98; N, 13.51.
4b:2 Mp 145–147ꢀC (CH2Cl2–hexane); 1H NMR (DMSO-d6) d 0.82 (d,
6H, -i-Bu), 1.86–2.13 (m, 1H, -CH(Me)2), 3.59 (d, 2H, i-Pr-CH2-), 5.57 (d,
1H, H-5, J ¼ 7.6), 7.42 (d, 1H, H-6, J ¼ 7.6), 11.07 (s, 1H, H-1); Anal. calc.
for C8H12N2O2.0.05H2O: C, 56.82; H, 7.21; N, 16.57. Found: C, 57.14; H,
7.21; N, 16.57.
4d:1a,2,8 Mp 200–202ꢀC (CH2Cl2–hexane) Lit.8 mp 202–204; H NMR
1
(DMSO-d6) d 1.78 (s, 3H, -Me), 4.95 (s, 2H, -Bn), 7.20–7.33 (m, 5H, -Ph),
7.35 (s, 1H, H-6), 11.00 (s, 1H, H-1); Anal. calc. for C12H12N2O2: C, 66.64;
H, 5.59; N, 12.95. Found: C, 66.34; H, 5.55; N, 12.75.

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JAIME-FIGUEROA ET AL.
4e:2 Mp 109–110ꢀC (CH2Cl2–hexane); 1H NMR (DMSO-d6) d 0.82 (d,
6H, -i-Bu), 1.77 (s, 3H, -Me), 1.90–2.15 (m, 1H, -CH(Me)2), 3.61 (d, 2H,
i-Pr-CH2-N), 7.28 (s, 1H, H-6), 10.84 (br. s, 1H, H-1); Anal. calc. for
C9H14N2O2.0.05 hex.; C, 60.01; H, 7.74; N, 15.05. Found: C, 59.85; H,
8.13; N, 14.80.
4g:2 Mp 160–161ꢀC (EtOAc); H NMR (DMSO-d6) d 4.98 (s, 2H,
1
-Bn), 7.20–7.31 (m, 5H, -Ph), 8.0 (s, 1H, H-6), 11.70 (br. s, 1H, H-1);
Anal. calc. for C11H9N2BrO2: C, 47.00; H, 3.23; N, 9.97. Found: C,
47.36; H, 3.27; N, 9.72.
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Received in the USA February 7, 2001

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