Efficient N-arylation and N-alkenylation of the five DNA/RNA nucleobases

Article abstract of DOI:10.1021/jo061694i

(Chemical Equation Presented) A general approach to N-arylation and N-alkenylation of all five DNA/RNA nucleobases at the nitrogen atom normally attached to the sugar moiety in DNA or RNA has been developed. Various protected or masked nucleobases engaged

Full text of DOI:10.1021/jo061694i

Efficient N-Arylation and N-Alkenylation of the Five DNA/RNA
Nucleobases
Mikkel F. Jacobsen, Martin M. Knudsen, and Kurt V. Gothelf*
Center for Catalysis and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry,
UniVersity of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
kVg@chem.au.dk
ReceiVed August 15, 2006
A general approach to N-arylation and N-alkenylation of all five DNA/RNA nucleobases at the nitrogen
atom normally attached to the sugar moiety in DNA or RNA has been developed. Various protected or
masked nucleobases engaged readily in the copper-mediated Chan-Lam-Evans-modified Ullmann
condensation with a range of different boronic acids at room temperature and were subsequently converted
to the corresponding deprotected or unmasked adducts. Different N3-protecting groups were examined in
the case of thymine, where the benzoyl group afforded the highest yields. A 4-alkylthio-substituted
pyrimidin-2(1H)-one served as both a cytosine and a uracil precursor and was N-arylated and N-alkenylated
in high yields. Adenine was efficiently and selectively N-arylated and N-alkenylated at the N9 position
by employing a bis-Boc-protected adenine derivative, while a bis-Boc-protected 2-amino-6-chloropurine
served as guanine precursor and could also be selectively N9-arylated and N9-alkenylated.
Introduction
bisaryl-like linkage to the nucleobase instead of a natural ribose
phosphate (DNA and RNA) or (2-aminoethyl)glycine peptide
(PNA) backbone. Furthermore, several N-arylpurines and N-
arylpyrimidines show interesting biological activities, such as
agonism and antagonism toward receptors and enzymes as well
as antiviral and antibacterial activities.6 Motivated by this, in
The ability to modify individual nucleobases is of major
importance both in the development of drugs1 and in the study
of nucleic acid function and structure.2 The interaction between
nucleobases in DNA and RNA has been extensively studied in
solution and in the solid state,3 and notably, surface studies using
scanning tunneling microscopy have emerged as a means for
investigating base pairing in self-assembled structures.4 Recent
efforts have focused on the synthesis and properties of nucleic
acid analogues incorporating N-aryl-modified nucleobases.5
These analogues feature a π electron-rich backbone with a
(6) N-Arylpurines: (a) Harada, H.; Asano, O.; Kawara, T.; Inoue, T.;
Horizoe, T.; Yasuda, N.; Nagata, K.; Murakami, M.; Nagaoka, J.; Kobayashi,
S.; Tanaka, I.; Abe, S. Bioorg. Med. Chem. 2001, 9, 2709-2726. (b)
Kumagai, T.; Okubo, T.; Kataoka-Okubo, H.; Chaki, S.; Okuyama, S.;
Nakazato, A. Bioorg. Med. Chem. 2001, 9, 1357-1363. (c) Moriguchi, I.;
Kanada, Y. Chem. Pharm. Bull. 1977, 25, 926-935. (d) Young, R. C.;
Jones, M.; Milliner, K. J.; Rana, K. K.; Ward, J. G. J. Med. Chem. 1990,
33, 2073-2080. (e) Brakta, M.; Murthy, D.; Ellis, L.; Phadtare, S. Bioorg
Med. Chem. Lett. 2002, 12, 1489-1492. (f) Baker, B. R.; Siebeneick, H.
U. J. Med. Chem. 1971, 14, 802-805. (g) Bakkestuen, A. K.; Gundersen,
L.-L.; Langli, G.; Liu, F.; Nolsøe, J. M. J. Bioorg. Med. Chem. Lett. 2000,
10, 1207-1210. (h) Gundersen, L.-L.; Nissen-Meyer, J.; Spilsberg, B. J.
Med. Chem. 2002, 45, 1383-1386. (i) Koppel, H. C.; Robins, R. K. J. Am.
Chem. Soc. 1958, 80, 2751-2755. (j) Koppel, H. C.; O’Brien, D. E.; Robins,
R. K. J. Am. Chem. Soc. 1959, 81, 3046-3051. (k) Sen, D.; Dasgupta, A.;
Sengupta, P. Indian J. Chem., Sect. B: Org. Chem. Incl. Med. Chem. 1985,
24B, 952-958. (l) Basyouni, W. M.; Hosni, H. M.; Helmy, S. M. Egypt. J.
Chem. 1999, 42, 587-598. (m) El-Bayouki, K. A. M.; Haggag, B.;
Basyouni, W. M. Egypt. J. Chem. 1990, 33, 243-253. N-Arylpyrimidines:
Brown, D. J. In ComprehensiVe Heterocyclic Chemistry - The Structure,
Reaction, Synthesis and Uses of Heterocyclic Compounds; Katritzky, A.
R., Rees, C. W., Eds.; Pergamon Press: New York, 1984; Vol. 3, p 57.
(1) For some recent reviews, see: (a) Kimura, K.-I.; Bugg, T. D. H.
Nat. Prod. Rep. 2003, 20, 252-273. (b) Simons, C.; Wu, Q.; Htar, T. T.
Curr. Top. Med. Chem. 2005, 5, 1191-1203.
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(3) Neidle, S. Nucleic Acid Structure and Recognition; Oxford University
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I.; Hammer, B.; Besenbacher, F. Angew. Chem., Int. Ed. 2005, 44, 2270-
2275. (b) Xu, S. L.; Dong, M.; Rauls, E.; Otero, R.; Linderoth, T. R.;
Besenbacher, F. Nano Lett. 2006, 6, 1434-1438.
(5) (a) Ueno, Y.; Kato, T.; Sato, K.; Ito, Y.; Yoshida, M.; Inoue, T.;
Shibata, A.; Ebihara, M.; Kitade, Y. J. Org. Chem. 2005, 70, 7925-7935.
(b) Sauter, G.; Stulz, E.; Leumann, C. HelV. Chim. Acta 1998, 81, 14-34.
(c) Sauter, G.; Leumann, C. HelV. Chim. Acta 1998, 81, 916-931.
10.1021/jo061694i CCC: $33.50 © 2006 American Chemical Society
Published on Web 10/25/2006
J. Org. Chem. 2006, 71, 9183-9190
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Jacobsen et al.
addition to our interest in DNA self-assembled nanostructures7
and the study of the self-organization of organic molecules on
surfaces,8 we pursued a general route to N-aryl and N-alkenyl
derivatives of all five DNA/RNA nucleobases.
SCHEME 1. Copper-Mediated C-N Bond Formation
Employing Boronic Acids
While methods for the synthesis of N-alkylpurines and
N-alkylpyrimidines are well developed,9 general and efficient
methods for the formation of N-aryl and N-alkenyl analogues
are lacking. Classically, the synthesis of N-aryl or N-alkenyl
derivatives of purines has centered on the heterocyclization of
suitable precursors, for example, chloropyrimidines, which are
often not readily available.10 In the synthesis of N-aryl or
N-alkenyl derivatives of pyrimidines, the reaction of suitable
pyrimidinones with aryliodonium salts has been exploited, both
in the case of cytosine11 and in the case of thymine/uracil;12
however, low yields of product are generally obtained. Because
of their limited scope and the often high temperatures employed
(>150 °C), the SNAr reactions of electron-deficient aryl halides
with nucleobases to furnish N-aryl nucleobases have only been
exploited in a few cases.13 Dahl and co-workers reported the
preparation of N-alkenyl nucleobases (enamines) by the
Horner-Wadsworth-Emmons reaction of phosphine oxide
derivatives of thymine and adenine.14 However, the basic
reaction conditions often resulted in low yields due to enolization
and decomposition.
different nitrogen compounds,16 only a few examples of
N-arylation of pyrimidines and purines employing the Chan-
Lam-Evans reaction have been described, and no examples of
N-alkenylation have, to the best of our knowledge, been
reported.
Schultz and co-workers reported the reaction of 2,6-dichloro-
purine with arylboronic acids,17 while Gundersen and Bakkes-
tuen accomplished the regioselective N9-arylation of various
purine structures with arylboronic acids, although attempts with
adenine itself were unsuccessful.18 Yu and co-workers recently
described the direct N-arylation of adenine and cytosine in an
aqueous solution, and although yields were generally good, the
low solubility of pure cytosine and adenine in aqueous MeOH
demanded a large solvent-substrate ratio.19 Evidently, the
notoriously low solubility of pure nucleobases in many solvents
makes their direct manipulation troublesome, and the presence
of several amino functionalities could potentially lead to a low
regioselectivity in any N-arylation and N-alkenylation reaction.
We envisioned that the use of readily available protected or
masked nucleobases in the copper-mediated N-arylation and
N-alkenylation with boronic acids could circumvent any com-
plications due to low solubility and the presence of multiple
amino functionalities and could provide a general and facile
route to N-aryl and N-alkenyl derivatives of nucleobases
(Scheme 2). The significantly improved solubility of the
protected coupling products allows standard chromatographic
purification to be carried out. Also, the use of protected or
masked nucleobases may prove advantageous in the case of any
subsequent transformations of the newly introduced aryl or
alkenyl moieties. Our goal was to perform selective N-arylation
and N-alkenylation at the nitrogen atom in the nucleobases
which is normally attached to the sugar moiety in DNA or RNA,
such that the products may engage in similar base pairing.
The Chan-Lam-Evans-modified Ullmann condensation has
proved to be among the most versatile and mild methods
available for C-N bond formation employing boronic acids as
aryl or alkenyl donors in the presence of copper species (Scheme
1).15 Although the reaction has been studied with a plethora of
(7) (a) Gothelf, K. V.; LaBean, T. H. Org. Biomol. Chem. 2005, 3, 4023-
4037. (b) Gothelf, K. V.; Brown, R. S. Chem. Eur. J. 2005, 11, 1062-
1069. (c) Gothelf, K. V.; Thomsen, A.; Nielsen, M.; Clo´, E.; Brown, R. S.
J. Am. Chem. Soc. 2004, 26, 1044-1046. (d) Nielsen, M; Thomsen, A. H.;
Clo´, E.; Kirpekar, F.; Gothelf, K. V. J. Org. Chem. 2004, 69, 2240. (e)
Brown, R. S.; Nielsen, M.; Gothelf, K. V. Chem. Commun. 2004, 13, 1464-
1465. (f) Nielsen, M.; Dauksaite, V.; Kjems, J.; Gothelf, K. V. Bioconjugate
Chem. 2005, 16, 681-685. (g) Blakskjær, P.; Gothelf, K. V. Org. Biomol.
Chem. 2006, 4, 3442-3447.
(8) Weigelt, S.; Busse, C.; Petersen, L.; Rauls, L.; Hammer, B.; Gothelf,
K. V.; Besenbacher, F.; Linderoth, T. R. Nat. Mater. 2006, 5, 112-117.
(9) N-Alkylpurines: (a) Kjellberg, J.; Johansson, N. G. Nucleosides
Nucleotides 1989, 8, 225-256 and references therein. (b) Nova´k, J.; Linhart,
I.; Dvorˇa´kova´, H. Eur. J. Org. Chem. 2004, 2738-2746. (c) Kalayanov,
G.; Jaksˇa, S.; Scarcia, T.; Kobe, J. Synthesis 2004, 12, 2076-2034. (d)
Zhong, M.; Nowak, I.; Cannon, J. F.; Robins, M. J. J. Org. Chem. 2006,
71, 4216-4221 and references therein. N-Alkylpyrimidines: (a) Ward, A.
D.; Baker, B. R. J. Med. Chem. 1977, 20, 88-92. (b) Ewing, D. F.; Glacon,
V.; Len, C.; Mackenzie, G. New J. Chem. 2005, 29, 1461-1468. (c) Zhang,
L.; Peritz, A.; Meggers, E. J. Am. Chem. Soc. 2005, 127, 4174-4175. (d)
Wu, F.; Buhendwa, M. G.; Weaver, D. F. J. Org. Chem. 2004, 69, 9307-
9309. (e) Diederichsen, U.; Weicherding, D.; Diezemann, N. Org. Biomol.
Chem. 2005, 6, 1058-1066.
Results and Discussion
Initial efforts focused on the N-arylation of thymine and on
choosing the optimal N3-protection group. Three different N3-
protection groups were examined, 4-tert-butylbenzyl, Boc, and
benzoyl (Bz). All three thymine derivatives are readily soluble
(10) Monographs and comprehensive reviews: (a) Lister, J. H. In The
Chemistry of Heterocyclic Coumpounds; Weissberger, A., Taylor, E. C.,
Eds.; Wiley-Interscience: New York, 1971; Vol. 24. (b) Shaw, G. In
ComprehensiVe Heterocyclic Chemistry - The Structure, Reaction, Synthesis
and Uses of Heterocyclic Compounds; Katritzky, A. R., Rees, C. W., Eds.;
Pergamon Press: New York, 1984; Vol. 5, pp 501-597. (c) Ewing, D. F.;
Mackenzie, G. In Second Supplements to the 2nd Edition of Rodd’s
Chemistry of Carbon Compounds; Sainsbury, M., Ed.; Elsevier Science B.
V.: Amsterdam, 1999; Vol. IV K(partial)/L, pp 127-179.
(15) Ley, S. V.; Thomas, A. W. Angew. Chem., Int. Ed. 2003, 42, 5400-
5449.
(16) Some recent examples: (a) Chiang, G. C. H.; Olsson, T. Org. Lett.
2004, 6, 3079-3082. (b) Sasaki, M.; Dalili, S.; Yudin, A. K. J. Org. Chem.
2003, 68, 2045-2047. (c) Yu, S.; Saenz, J.; Srirangam, J. K. J. Org. Chem.
2002, 67, 1699-1702. (d) Antilla, J. C.; Buchwald, S. L. Org. Lett. 2001,
3, 2077-2079. (e) Lam, P. Y. S.; Vincent, G.; Clark, C. G.; Deudon, S.;
Jadhav, P. K. Tetrahedron Lett. 2001, 42, 3415-3418. (f) Collman, J. P.;
Zhong, M. Org. Lett. 2000, 2, 1233-1236. (g) Mederski, W. W. K. R.;
Lefort, M.; Germann, M.; Kux, D. Tetrahedron 1999, 55, 12757-12770.
(17) Ding, S.; Gray, S. N.; Ding, Q.; Schultz, P. G. Tetrahedron Lett.
2001, 42, 8751-8755.
(18) Bakkestuen, A. K.; Gundersen, L.-L. Tetrahedron Lett. 2003, 44,
3359-3362.
(19) Yue, Y.; Zheng, Z.-G.; Wu, B.; Xia, C.-Q.; Yu, X.-Q. Eur. J. Org.
Chem. 2005, 5154-5157.
(11) Stig, A. J.; Synne, R.; Tore, B. J. Chem. Soc., Perkin Trans. 1 1999,
3265-3268.
(12) Zhou, T.; Li, T.-C.; Chen, Z.-C. HelV. Chim. Acta 2005, 88, 290-
296.
(13) (a) Gondela, A.; Walczak, K. Tetrahedron: Asymmetry 2005, 16,
2107-2112. (b) Boga, C.; Bonmartini, A. C.; Forlani, L.; Modarelli, V.;
Righi, L.; Sgarabotto, P. J. Chem. Res., Miniprint 2001, 12, 1217-1231.
(14) Boesen, T.; Madsen, C.; Henriksen, U.; Dahl, O. J. Chem. Soc.,
Perkin Trans. 1 2000, 2015-2021.
9184 J. Org. Chem., Vol. 71, No. 24, 2006

N-Arylation and N-Alkenylation of Nucleobases
SCHEME 2. Strategy for the N-Arylation and N-Alkenylation of Nucleobases
SCHEME 3. Synthesis of N3-(4-tert-Butylbenzyl)-Protected Thymine 1
SCHEME 4. Synthesis of N3-Boc-Protected Thymine 4
TABLE 1. Influence of N3 Protection Group on N-Arylation of
detected by TLC. Notably, the Bz-protection group proved
Thymine
superior compared to Boc or 4-tert-butylbenzyl. For example,
the yields of products 7a-c improved from a 57% yield with
4-tert-butylbenzyl (entry 1) to an excellent 92% yield (entry 3)
with Bz, with Boc giving a slightly lower yield (entry 2). Hence,
mainly the Bz derivative 6 was chosen for further studies. For
any given protection group, the yield decreased in the order H
> Me > OMe with respect to the para-substituted arylboronic
acid employed, demonstrating the sensitivity of the reaction to
the nature of the arylboronic acid.
Gratifyingly, the reactions of 6 with various aryl- and
alkenylboronic acids proved to be of wide scope and furnished
the desired products 8c-j in up to a 98% yield (Table 2).
Various groups and substitution patterns on the aryl ring were
tolerated, including electron-rich ortho-substituted arylboronic
acids (entry 3). Furthermore, the Bz-protected uracil derivative
921 could also be N-arylated and N-alkenylated in high yields
(entries 11 and 12).
protection
group (PG)
thymine
derivative
N-aryl
product
yield
(%)
entry
R
1
2
3
4
5
6
7
H
H
H
Me
Me
4-tBu-Bn
Boc
Bz
4-tBu-Bn
Bz
4-tBu-Bn
Bz
1
4
6
1
6
1
6
7a
7b
7c
7d
7e
7f
57
87
92
55
87
31
66
OMe
OMe
7g
Next, we examined suitable cytosine derivatives for the
N-arylation reaction. However, the use of the known imino
derivative 10 (from the condensation of cytosine with N,N-
dimethylformamide diethyl acetal)22 was unsuccessful and led
only to intractable product mixtures, supposedly because of the
incompatibility of the imino functionality with the reaction
conditions (Chart 1). On the other hand, the commercially
available Bz derivative 11 led to mixtures of mono- and di-
arylated products in low yields. Fortunately, 4-alkylthio-
substituted pyrimidin-2(1H)-ones readily undergo substitution
with methanolic ammonia, rendering them useful precursors of
cytosine derivatives.23 In addition, their reaction with aq HCl
in common organic solvents, such as CH2Cl2, THF, and EtOAc.
The N3-(4-tert-butylbenzyl)-protected thymine 1 was readily
obtained in three steps from thymine 2 via the known N1-mono-
Boc derivative 3 (Scheme 3).20 The N3-Boc-protected thymine
4 was obtained by selective removal of the N1-Boc group from
bis-Boc derivative 5 with K2CO3 (Scheme 4).
The copper-mediated reactions of 1, 4, and the known N3-
benzoyl thymine 621 with arylboronic acids were attempted
under standard conditions employing pyridine as the ligand/
base and CH2Cl2 as the solvent (Table 1). The reactions were
generally left for 3 days or until no further progress could be
(20) Jaime-Figueroa, S.; Zamilpa, A.; Guzman, A.; Morgans, D. J. Synth.
Commun. 2001, 31, 3739-3746.
(21) Frieden, M.; Giraud, M.; Reese, C. B.; Song, Q. J. Chem. Soc.,
Perkin Trans. 1 1998, 2827-2832.
(22) Hosmane, R. S.; Leonard, N. J. J. Org. Chem. 1981, 46, 1457-
1465.
(23) Barrio, J. R.; Bryant, J. D.; Keyser, G. E. J. Med. Chem. 1980, 23,
572-574.
J. Org. Chem, Vol. 71, No. 24, 2006 9185

Jacobsen et al.
TABLE 2. N-Arylation and N-Alkenylation of N3-Protected Thymine and Uracil
conditions, it furnished the desired N1-arylated and N1-alkenyl-
ated products 13 in good to high yields (Table 3). The reactions
proceeded with complete regioselectivity since in no case could
the regioisomeric N3 products be observed.25
CHART 1. Derivatives of Cytosine and Guanine Tested in
the N-Arylation Reaction
In our efforts to N-arylate and N-alkenylate adenine, we were
provided, by the work of Garner and Dey on the synthesis of
Boc-protected purines, with the bis-Boc-protected adenine 14
which underwent facile N-arylation and N-alkenylation with
different boronic acids (Table 4).26 Bis-Boc-protected adenine
14 is easily soluble in common organic solvents and obtained
in two steps from adenine in an 87% overall yield.26 By
changing the base/ligand to Et3N and the solvent to DMF,
improved yields of the N9-arylated products could be obtained
(compare entries 1-3). In no case could the regioisomeric N7-
1
aryl or N7-alkenyl products be detected by H NMR analysis
of the crude reaction mixture, and the structure of the products
was unambiguously confirmed by single-crystal X-ray crystal-
lographic analysis of 15f.27 Since the N-arylated and N-
or hydroxides effectively affords the corresponding uracil
derivatives.24 The readily soluble 4-allylthio derivative 12 can
be obtained in a high yield (80%) from commercially available
4-thiouracil,24 and when subjected to the standard reaction
(25) NOE measurements on the products of 13 confirmed that exclusively
N1-arylation and N1-alkenylation had taken place.
(24) Mizutani, M.; Sanemitsu, Y.; Tamaru, Y.; Yoshida, Z.-I. Tetrahedron
1985, 41, 5289-5294.
(26) Dey, S.; Garner, P. J. Org. Chem. 2000, 65, 7697-7699.
(27) See Supporting Information.
9186 J. Org. Chem., Vol. 71, No. 24, 2006

N-Arylation and N-Alkenylation of Nucleobases
TABLE 3. N-Arylation and N-Alkenylation of Cytosine/Uracil
Precursor 12
TABLE 4. N-Arylation and N-Alkenylation of Bis-Boc-adenine 14
alkenylated purines can, themselves, serve as ligands for
Cu(II),28 we speculated that the failure to remove any copper
salts prior to purification of the products by flash chromatog-
raphy may render the products less mobile by complexation to
Cu(II) species and could potentially lower the yields. Hence, a
treatment with an aqueous solution of the strongly Cu(II)-
chelating agent EDTA was included in the workup of the
reaction mixtures.
a CH2Cl2 was used as the solvent. b Pyridine (2.0 equiv) was used as
the base/ligand, and CH2Cl2 was used as the solvent.
TABLE 5. N-Arylation and N-Alkenylation of Guanine
Precursor 18
The modification of guanine is, in itself, a major challenge
because of its insolubility in almost all solvents and its
polyfunctional nature with imidazole, amide, and guanidine
substructures. Johansson and co-workers have developed several
guanine precursors for the N7- and N9-alkylation of the imidazole
substructure, for example, 16 and 17 (Chart 1) which, subsequent
to alkylation, can be converted to the unmasked guanine
derivatives following treatment with methanolic KOH.29 Un-
fortunately, these protected guanine derivatives proved unstable
to the reaction conditions. We, therefore, turned our attention
to the bis-Boc-purine 18 reported by Garner and Dey, which
can be obtained in two simple steps from 2-amino-6-chloropu-
rine in an 84% overall yield.26 We envisaged that the products
from 18 may be converted directly to the corresponding guanine
derivatives. Subjection of 18 to the standard reaction conditions
with various boronic acids furnished the desired products 19 in
fair to good yields (Table 5). As in the case of 14, the use of
(28) For some examples, see: (a) Garcia-Teran, J. P.; Castillo, O.; Luque,
A.; Garcia-Couceiro, U.; Roman, P.; Lloret, F. Inorg. Chem. 2004, 43,
5761-5770. (b) Song, B.; Zhao, J.; Griesser, R.; Meiser, C.; Sigel, H.;
Lippert, B. Chem. Eur. J. 1999, 5, 2374-2387. (c) Steinkopf, S.; Liu, Q.;
Froeystein, N. A.; Sletten, E. Acta Chem. Scand. 1992, 46, 446-450. (d)
Jitsukawa, K.; Mizutani, M.; Arii, H.; Kubo, I.; Izu, Y.; Ozawa, T.; Masuda,
H. Chem. Lett. 2004, 33, 1302-1303.
(29) (a) Kjellberg, J.; Hagberg, C.-E.; Malm, A.; Noren, J. O.; Johansson,
N. G. Acta Chem. Scand. 1986, B40, 310-312. (b) Kobe, J.; Kjellberg, J.;
Johansson, N. G. Acta Chem. Scand. 1987, B41, 564-568.
a Et3N was used as the base/ligand, and DMF was used as the solvent.
Et3N and DMF instead of pyridine and CH2Cl2 enhanced the
yield of products in some cases (entries 4 and 5). The structure
of the N9-arylated and N9-alkenylated product was unambigu-
ously confirmed by single-crystal X-ray crystallographic analysis
of 19b.27
J. Org. Chem, Vol. 71, No. 24, 2006 9187

Jacobsen et al.
SCHEME 6. Conversion of 15c,e and 19a to N-Arylated
SCHEME 5. Conversion of 7c, 8c, and 13f,e to N-Arylated
Nucleobases 20-23
Nucleobases 24-26
Conclusions
Protected or masked derivatives of the five nucleobases,
thymine, uracil, cytosine, adenine, and guanine, have been
examined for their ability to undergo copper-mediated N-
arylation and N-alkenylation with various boronic acids (Chan-
Lam-Evans-modified Ullmann condensation). The reactions
tolerated various substitution patterns on the arylboronic acids
including ortho-substitution and electron-donating groups. The
products were obtained in good to high yields and could
subsequently be readily converted to the corresponding depro-
tected or unmasked N-arylated or N-alkenylated nucleobases.
This constitutes the first general approach to N-arylated or
N-alkenylated derivatives of all five DNA/RNA nucleobases.
Further work will focus on the implementation of a protocol
catalytic in a copper reagent and on the synthesis of suitable
N-arylated or N-alkenylated nucleobases, including dimers and
trimers of nucleobases linked via rigid aryl or alkenyl moieties,
for the study of their interaction with DNA and of their behavior
on surfaces.
The conversion of the protected or masked N-arylated
pyrimidines 7c, 8c, 13f, and 13e to the free N-arylated
nucleobases 20-23 was efficiently accomplished as outlined
in Scheme 5. The products 7c and 8c from protected thymine
6 could be deprotected using either hydrazine hydrate30 or KOH,
while the masked cytosine/uracil derivatives 13f,e were trans-
formed into N-arylated cytosine 22 and N-arylated uracil 23,
employing NH3-saturated MeOH and aq HCl, respectively.
The deprotection of the bis-Boc-protected adenine products
15 was unsuccessful by even prolonged exposure to conven-
tional TFA-CH2Cl2 solution. Fortunately, the bis-Boc-protected
adenine derivatives 15c,e were readily converted to the free
N-arylated nucleobases 24 and 25 using either treatment with
HCl or treatment with KOH, respectively (Scheme 6). The
simultaneous removal of the bis-Boc protection and conversion
of the chloropurine substructure in 19a to N9-phenylguanine 2631
was facilitated by treatment with an aq HCl-AcOH mixture.
Notably, 26 is an excellent irreversible inhibitor of both guanine
deaminase32 and xanthine oxidase.33
Experimental Section
Typical Procedure for the N-Arylation and N-Alkenylation
of Nucleobases: 3-Benzoyl-1-(4-iodophenyl)-5-methylpyrimi-
dine-2,4(1H,3H)-dione (8h). To a stirred suspension of dry
Cu(OAc)2 (109 mg, 0.60 mmol), N3-benzoylthymine 6 (92.1 mg,
0.40 mmol), p-iodobenzeneboronic acid (198 mg, 0.80 mmol), and
activated 3 Å molecular sieves (200 mg) in dry CH2Cl2 (3.0 mL)
was added pyridine (65 µL, 0.80 mmol) at rt. The mixture was
stirred vigorously for 74 h at rt in the presence of air. The reaction
mixture was diluted with CH2Cl2 (15 mL), filtered through a pad
of Celite, and washed with water (15 mL) in the presence of EDTA
(200 mg). The colorless organic phase was dried over MgSO4 and
was evaporated to dryness in vacuo. The residue was subjected to
(30) (a) Boger, D. L.; Machiya, K. J. Am. Chem. Soc. 1992, 114, 10056-
10058. (b) Boger, D. L.; McKie, J. A.; Nishi, T.; Ogiku, T. J. Am. Chem.
Soc. 1997, 119, 311-325.
(31) Baker, B. R.; Wood, W. F. J. Med. Chem. 1967, 10, 1101-1105.
(32) Baker, B. R.; Santi, D. V. J. Med. Chem. 1967, 10, 62-64.
(33) Baker, B. R.; Kozma, J. J. Med. Chem. 1967, 10, 682-685.
9188 J. Org. Chem., Vol. 71, No. 24, 2006

N-Arylation and N-Alkenylation of Nucleobases
flash chromatography (40:1 CH2Cl2-EtOAc) to afford 8h (168 mg,
97%) as a white solid: Rf ) 0.71 (10:1 CH2Cl2-EtOAc); mp 246-
was heated at 100 °C in a sealed tube for 4 h. The mixture was
cooled and was evaporated to dryness in vacuo. The residue was
subjected to flash chromatography (1:1 CH2Cl2-EtOAc) to afford
20 (18 mg, 99%) as a white solid: Rf ) 0.51 (1:1 CH2Cl2-EtOAc);
1
247 °C (from CH2Cl2); H NMR (400 MHz, DMSO-d6) δ 8.08
(dd, J ) 1.5, 8.5 Hz, 2H), 7.89 (d, J ) 8.5 Hz, 2H), 7.88 (s, 1H),
7.79 (tt, J ) 1.5, 7.5 Hz, 1H), 7.61 (dd, J ) 7.5, 8.5 Hz, 2H), 7.35
(d, J ) 8.5 Hz, 2H), 1.89 (d, J ) 1.0 Hz, 3H); 13C NMR (100
MHz, DMSO-d6) δ 169.5, 163.0, 148.7, 142.0, 138.1, 138.0 (2C),
135.5, 131.1, 130.5 (2C), 129.4 (2C), 129.2 (2C), 109.3, 94.7, 11.8.
HRMS (ES) m/z: [M + Na]+ calcd for C18H13IN2O3Na, 454.9869;
found, 454.9872.
1
mp 199-200 °C (lit. mp 198-200 °C;12 from CH2Cl2); H NMR
(400 MHz, CDCl3) δ 8.94 (br s, 1H), 7.46-7.51 (m, 2H), 7.40-
7.44 (m, 1H), 7.34-7.36 (m, 2H), 7.19 (q, J ) 1.5 Hz, 1H), 1.98
(s, 3H); 13C NMR (100 MHz, CDCl3) δ 164.2, 150.3, 140.8, 138.6,
129.6 (2C), 128.8, 126.4 (2C), 111.2, 12.4. HRMS (ES) m/z: MH+
calcd for C11H11N2O2, 203.0821; found, 203.0820.
3-(4-tert-Butylbenzyl)-5-methylpyrimidine-2,4(1H,3H)-di-
one (1). To a stirred solution of thymine (2.00 g, 15.9 mmol) in
MeCN (100 mL) was added DMAP (19 mg, 0.159 mmol) followed
by Boc2O (3.47 g, 15.9 mmol) at rt. The reaction mixture was stirred
for 3 h. The solvent was removed by evaporation in vacuo. The
crude product 3 was dissolved in DMF (75 mL), and NaH (760
mg, 60% w/w in oil, 19.0 mmol) was cautiously added at 0 °C.
The mixture was stirred for 30 min at 0 °C, and 4-tert-butyl-
benzylbromide (2.9 mL, 16 mmol) was added dropwise. The
reaction mixture was allowed to warm to rt, and it was stirred for
30 min. The mixture was diluted with water and was extracted
several times with EtOAc. The combined extracts were dried over
MgSO4 and were evaporated to dryness in vacuo. The crude product
was dissolved in MeOH (30 mL), and powdered K2CO3 (1.11 g,
8.00 mmol) was added. The mixture was stirred for 24 h at rt. The
mixture was evaporated to dryness, and the residue was extracted
several times with CH2Cl2. The combined extracts were filtered
and were evaporated to dryness in vacuo to leave the pure 1 (3.55
g, 13.0 mmol) as a white solid: mp 197-199 °C (from CH2Cl2);
1H NMR (400 MHz, DMSO-d6) δ 7.34 (s, 1H), 7.30 (d, J ) 8.2
Hz, 2H), 7.21 (d, J ) 8.2 Hz, 2H), 4.93 (s, 2H), 1.79 (s, 3H), 1.23
(s, 9H); 13C NMR (100 MHz, DMSO-d6) δ 163.8, 151.5, 149.4,
136.7, 134.5, 127.5 (2C), 125.0 (2C), 107.2, 42.5, 34.1, 31.1, 12.5
(3C). HRMS (ES) m/z: MH+ calcd for C16H21N2O2, 273.1603;
found, 273.1610.
Di-tert-butyl-5-methyl-2,4-dioxopyrimidine-1,3(2H,4H)-dicar-
boxylate (5). Thymine 2 (5.0 g, 22.1 mmol), di-tert-butyl dicar-
bonate (13.0 g, 65 mmol), pyridine (8 mL), and MeCN (40 mL)
were stirred together for 4 h at 55 °C. The reaction mixture was
concentrated in vacuo, and the residue was partitioned between
CH2Cl2 (50 mL) and water (50 mL). The organic layer was
separated, and the aqueous phase was extracted twice with CH2Cl2
(25 mL). The combined organic layers were dried over MgSO4
and filtered, and the solvent was removed by evaporation in vacuo.
The residue was purified by flash chromatography (CH2Cl2)
affording 5 (6.5 g, 90%) as a white solid: mp 147-148 °C (from
CH2Cl2); 1H NMR (400 MHz, CDCl3) δ 7.68 (s, 1H), 1.94 (s, 3H),
1.58 (s, 18H); 13C NMR (100 MHz, CDCl3) δ 161.3, 148.5, 147.7,
145.9, 134.8, 111.9, 87.5, 87.2, 28.0, 27.6, 12.8 (3C), 12.8 (3C).
HRMS (ES) m/z: [M + Na]+ calcd for C15H22N2O6Na, 349.1376;
found, 349.1380.
5-Methyl-1-(2,4,5-trimethylphenyl)pyrimidine-2,4(1H,3H)-di-
one (21). To a stirred solution of 8c (52.3 mg, 0.15 mmol) in
EtOH-H2O (3.0 mL, 2:1 v/v) was added KOH (84 mg, 1.50 mmol),
and the mixture was heated at 70 °C for 4 h. The mixture was
cooled and was extracted twice with CH2Cl2. The combined extracts
were dried over MgSO4 and were evaporated to dryness in vacuo.
The residue was subjected to flash chromatography (1:1 CH2Cl2-
EtOAc) to afford 21 (31.8 mg, 87%) as a white solid: Rf ) 0.68
1
(1:1 CH2Cl2-EtOAc); mp 204-205 °C (from CH2Cl2); H NMR
(400 MHz, CDCl3) δ 8.93 (s, 1H), 7.08 (s, 1H), 7.00 (q, J ) 1.0
Hz, 1H), 6.96 (s, 1H), 2.25 (s, 3H), 2.24 (s, 3H), 2.14 (s, 3H), 1.95
(d, J ) 1.0 Hz, 3H); 13C NMR (100 MHz, CDCl3) δ 164.5, 150.2,
141.3, 138.3, 135.9, 135.0, 132.5, 132.5, 128.2, 110.6, 19.5, 19.3,
17.0, 12.4. HRMS (ES) m/z: MH+ calcd for C14H17N2O2, 245.1290;
found, 245.1285.
4-Amino-1-(4-fluoro-3-methylphenyl)pyrimidin-2(1H)-one (22).
Compound 13f was dissolved in MeOH (5.0 mL), and the solution
was saturated with NH3 by bubbling NH3 gas through it at rt. The
solution was heated in a sealed tube at 100 °C for 19 h. The resulting
white suspension was cooled, and Et2O (15 mL) was added. The
mixture was further cooled in an ice bath and filtered. The white
solid was washed several times with Et2O and was dried in vacuo
to afford pure 22 (63.7 mg, 97%) as a white solid: mp > 250 °C;
1H NMR (400 MHz, DMSO-d6) δ 7.59 (d, J ) 7.50 Hz, 1H), 7.27-
7.32 (m, 3H), 7.18-7.20 (m, 2H), 5.78 (d, J ) 7.5 Hz, 1H), 2.25
(s, 3H); 13C NMR (100 MHz, DMSO-d6) δ 166.2, 159.2, 155.0,
145.8, 137.3, 129.8 (d, J ) 5.3 Hz), 126.0 (d, J ) 8.4 Hz), 124.7
(d, J ) 18.3 Hz), 115.1 (d, J ) 23.6 Hz), 94.1, 14.1. HRMS (ES)
m/z: MH+ calcd for C11H11FN3O, 220.0886; found, 220.0890.
1-(4-Iodophenyl)pyrimidine-2,4(1H,3H)-dione (23). Compound
13e (100 mg, 0.27 mmol) was dissolved in a mixture of aq HCl (1
mL, 37% w/w) and EtOH (2 mL) and was refluxed for 3 h. The
reaction mixture was cooled to rt and was partitioned between
CH2Cl2 (25 mL) and water (10 mL). The organic layer was
separated, and the aqueous phase was extracted twice with CH2Cl2
(25 mL). The combined extracts were dried over MgSO4 and
evaporated to dryness in vacuo. The residue was washed with Et2O
(10 mL) and was filtered, yielding 23 (67 mg, 79%) as a white
1
solid: mp 291-292 °C; H NMR (400 MHz, DMSO-d6) δ 11.4
(br s, 1H), 7.82 (d, J ) 9.0 Hz, 2H), 7.67 (d, J ) 8.0 Hz, 1H), 7.22
(d, J ) 9.0 Hz, 2H), 5.66 (d, J ) 8.0 Hz, 1H); 13C NMR (100
MHz, DMSO-d6) δ 164.3, 150.9, 145.8, 139.3, 138.6 (2C), 129.8
(2C), 102.5, 95.0. HRMS (ES) m/z: MH+ calcd for C10H8IN2O2,
314.9630; found, 314.9639.
tert-Butyl-5-methyl-2,6-dioxo-2,3-dihydropyrimidine-1(6H)-
carboxylate (4). Compound 5 (6.0 g, 18.4 mmol) was dissolved
in dioxane (20 mL), and a solution of K2CO3 (3.8 g, 27.6 mmol)
in water (10 mL) was slowly added. After 40 min, the reaction
was quenched by the addition of glacial acetic acid (10 mL). The
reaction mixture was extracted with CH2Cl2 three times. The
combined extracts were dried over MgSO4 and filtered, and the
solvents were removed by evaporation in vacuo. The residue was
subjected to flash chromatography (9:1 CH2Cl2-EtOAc) yielding
4 (1.4 g, 34%) as a white solid: Rf ) 0.2 (9:1 CH2Cl2-EtOAc);
9-(4-Methoxyphenyl)-9H-purin-6-amine (24).34 To a stirred
solution of 15c (57.3 mg, 0.13 mmol) in MeOH (3.0 mL) was added
carefully AcCl (185 µL, 2.6 mmol) at rt. The mixture was stirred
for 72 h, and the white precipitate was filtered from the solution,
washed several times with Et2O, and dried in vacuo to afford pure
1
24 (24.2 mg, 77%) as a white solid: mp > 290 °C (decomp); H
NMR (400 MHz, DMSO-d6) δ 9.65 (br s, 1H), 8.99 (br s, 1H),
8.80 (s, 1H), 8.55 (s, 1H), 7.69 (d, J ) 9.0 Hz, 2H), 7.16 (d, J )
9.0 Hz, 2H), 3.83 (s, 3H); 13C NMR (100 MHz, DMSO-d6) δ 159.3,
150.7, 148.2, 145.5, 143.3, 126.5, 125.7 (2C), 118.7, 114.8 (2C),
55.6. HRMS (ES) m/z: MH+ calcd for C12H12N5O, 242.1042;
found, 242.1047.
1
mp 310-312 °C (from CH2Cl2); H NMR (400 MHz, CDCl3) δ
9.99 (br s, 1H), 7.06 (s, 1H), 1.92 (s, 3H), 1.60 (s, 9H); 13C NMR
(100 MHz, CDCl3) δ 162.1, 151.0, 148.1, 136.1, 110.8, 87.2, 27.7,
12.5 (3C). HRMS (ES) m/z: [M + Na]+ calcd for C10H14N2O4Na,
249.0851; found, 249.0841.
5-Methyl-1-phenylpyrimidine-2,4(1H,3H)-dione (20).12 To a
stirred solution of 7c (27.6 mg, 0.090 mmol) in MeOH (2.0 mL)
was added hydrazine hydrate (58 µL, 1.20 mmol). The clear solution
(34) Young, R. C.; Jones, M.; Milliner, K. J.; Rana, K. K.; Ward, J. G.
J. Med. Chem. 1990, 33, 2073-2080.
J. Org. Chem, Vol. 71, No. 24, 2006 9189

Jacobsen et al.
9-(4-Bromophenyl)-9H-purin-6-amine (25).19 To a stirred
solution of 15e (123 mg, 0.25 mmol) in MeOH (2.5 mL) was added
KOH (140 mg, 2.50 mmol). The mixture was heated at 50 °C for
19 h. The white suspension was cooled and filtered. The white
precipitate was washed with MeOH and Et2O and dried in vacuo
to afford pure 25 (65.4 mg, 90%) as a white solid: mp > 280 °C
(decomp); 1H NMR (400 MHz, DMSO-d6) δ 8.62 (s, 1H), 8.22 (s,
1H), 7.92 (d, J ) 9.0 Hz, 2H), 7.79 (d, J ) 9.0 Hz, 2H), 7.44 (br
s, 2H); 13C NMR (100 MHz, DMSO-d6) δ 156.4, 153.3, 149.0,
139.4, 134.5, 132.4 (2C), 124.7 (2C), 120.0, 119.3. HRMS (ES)
m/z: MH+ calcd for C11H979BrN5, 290.0041; found, 290.0050.
2-Amino-9-phenyl-1H-purin-6(9H)-one (26).31 To a stirred
suspension of 19a (89.2 mg, 0.20 mmol) in AcOH (3.0 mL) was
added carefully aq HCl (0.6 mL, 37% w/w), and the mixture was
heated at 90 °C for 17 h. The solution was cooled and was co-
evaporated twice with toluene (∼15 mL) to dryness in vacuo. The
crude product was dissolved in minimum MeOH and was evapo-
rated with silica gel (∼0.5 g) to dryness. The resulting powder was
subjected to flash chromatography (EtOAc f 200:40:1 EtOAc-
MeOH-Et3N f 10:10:1 EtOAc-MeOH-Et3N) to yield 26 (39.5
mg, 87%) as a white powder: Rf ) 0.19 (200:40:1 EtOAc-
MeOH-Et3N); mp > 300 °C (decomp); 1H NMR (400 MHz,
DMSO-d6) δ 10.79 (br s, 1H), 8.05 (s, 1H), 7.72 (d, J ) 7.5 Hz,
2H), 7.54 (t, J ) 7.5 Hz, 2H), 7.42 (t, J ) 7.5 Hz, 1H), 6.61 (br s,
2H); 13C NMR (100 MHz, DMSO-d6) δ 156.9, 153.9, 150.9, 136.4,
135.1, 129.3 (2C), 127.5, 123.7 (2C), 117.2; HRMS (ES) m/z: MH+
calcd for C11H10N5O, 228.0885; found, 228.0892.
Acknowledgment. We thank Dr. Jacob Overgaard for the
X-ray crystallographic analysis. Financial support for this work
by the Danish Technical Research Council, the Danish National
Research Foundation Center: Center for Catalysis, and the
Carlsberg Foundation is gratefully acknowledged.
Supporting Information Available: General experimental
methods, full characterization of compounds, ORTEP presentations
of 15f and 19b, and copies of 1H and 13C NMR spectra. This
materialisavailablefreeofchargeviatheInternetathttp://pubs.acs.org.
JO061694I
9190 J. Org. Chem., Vol. 71, No. 24, 2006