Substituent Effects on Pyrid-2-yl Ureas toward Intramolecular Hydrogen Bonding and Cytosine Complexation

Article abstract of DOI:10.1021/jo0355808

Equilibria between two conformational isomers of pyrid-2-yl ureas, the (E,Z) and (Z,Z) forms, have been studied in DMF-d₇ at -70 °C. Most of them show a small preference for the (E,Z) form with an equilibrium constant K_i around 1-2. However, the K_i value for 1-methyl-2-(3-(pyrid-2-yl)ureido)pyridinium iodide (12) was found to be 14.2 ± 1.2. That is 1 order of magnitude larger than those of the others, which indicates that the positively charged 1-methylpyridinium-2-yl substituent would facilitate the (E,Z) form formation. Pyrid-2-yl ureas bind cytosine in DMF-d₇ with binding constants K_B ranging from 30 to 1700 M^-1. Electron withdrawing substituents, such as the 4-O ₂NC₆H₄- or 1-methylpyridinium-4-yl substituent, preferentially facilitate the intermolecular cytosine complexation with large binding constants.

Full text of DOI:10.1021/jo0355808

Su bstitu en t Effects on P yr id -2-yl Ur ea s tow a r d In tr a m olecu la r
Hyd r ogen Bon d in g a n d Cytosin e Com p lexa tion
Chia-Hui Chien, Man-kit Leung,* J en-Kuan Su, Gene-Hsiang Li, Yi-Hung Liu, and Yu Wang
Department of Chemistry, National Taiwan University, Taipei, Taiwan 106, Republic of China
mkleung@ntu.edu.tw
Received October 28, 2003
Equilibria between two conformational isomers of pyrid-2-yl ureas, the (E,Z) and (Z,Z) forms, have
been studied in DMF-d7 at -70 °C. Most of them show a small preference for the (E,Z) form with
an equilibrium constant Ki around 1-2. However, the Ki value for 1-methyl-2-(3-(pyrid-2-yl)ureido)-
pyridinium iodide (12) was found to be 14.2 ( 1.2. That is 1 order of magnitude larger than those
of the others, which indicates that the positively charged 1-methylpyridinium-2-yl substituent would
facilitate the (E,Z) form formation. Pyrid-2-yl ureas bind cytosine in DMF-d7 with binding constants
KB ranging from 30 to 1700 M-1. Electron withdrawing substituents, such as the 4-O2NC6H4- or
1-methylpyridinium-4-yl substituent, preferentially facilitate the intermolecular cytosine complex-
ation with large binding constants.
In tr od u ction
(Scheme 1), an important hydrogen bonding unit for DNA
binding.7 Pyrid-2-yl ureas are known to have significant
biological activity in various dimensions, including an-
ticancer properties.8 Although the (Z,Z) form of pyrid-2-
yl urea contains an ADD hydrogen bonding array9 that
is complementary to the array of cytosine, their binding
is hindered by a competitive intramolecular hydrogen
bond between the pyridyl nitrogen and the ureido hy-
drogen that stabilizes the pyrid-2-yl urea in the (E,Z)
form.10,11 To make the binding more effective, substitu-
ents that could preferentially enhance the cytosine com-
plexation over the intramolecular hydrogen bonding
interaction are desired.
It has long been known that hydrogen bonds are
responsible for the intermolecular and intramolecular
order in carbohydrates,1 proteins,2 and nucleic acids.3
Many artificial receptors that employ hydrogen bond
centers or arrays as the recognition and binding elements
have been designed and synthesized.4 In particular,
molecules containing appropriate hydrogen arrays have
recently been used to harpoon the unpaired or bulged
bases in duplex DNA, which arise either from replication
error or from recombination of single stranded DNAs that
are not completely complementary to each other. For
example, 2-acylamino-1,8-naphthyridine derivatives have
been used to recognize single guanine bulges or to induce
DNA hairpins.5 Since our interest in the chemistry of
organic urea continues,6 we have examined the possibility
of using pyrid-2-yl urea as a receptor to recognize cytosine
Resu lts a n d Discu ssion
Syn th esis of th e P yr id -2-yl Ur ea s. To understand
the substituent effects, we explored a series of substituted
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10.1021/jo0355808 CCC: $27.50 © 2004 American Chemical Society
Published on Web 02/14/2004
1866
J . Org. Chem. 2004, 69, 1866-1871

Substituent Effects on Pyrid-2-yl Ureas
SCHEME 1
SCHEME 2
F IGURE 1. ORTEP of 12.
SCHEME 3
F IGURE 2. ORTEP of 13.
respectively, by methylation of the pyridyl substituent
with methyl iodide in DMSO.14 Interestingly, the reaction
stopped at monomethylation to give the desired products.
Their structures were further confirmed by X-ray crystal-
lographic analysis.
Sin gle-Cr ysta l X-r a y Cr ysta llogr a p h ic An a lyses
of 12 a n d 13. Single crystals of 12 and 13 were prepared
by slow evaporation of the methanol solutions. Crystals
of 12 are triclinic with the space group P1h and Z ) 4.
Crystals of 13 are monoclinic with the space group P21/n
and Z ) 4. Their ORTEP drawings are shown in Figures
1 and 2. While 13 exists in an extended (Z,Z) form in
the crystal lattice, 12 shows an (E,Z) form with N(1)H
intramolecularly hydrogen bonded to the pyridine nitro-
gen N(4). Both compounds in the crystal lattice are
planar with the pyridine rings coplanar with the ureido
group.
SCHEME 4
In compound 12, the C-N bond length for C(2)-N(1)
was found to be 1.37 Å, which is shorter than the C-N
bond length of 1.39 Å for C(8)-N(2). This result sug-
gested that the contribution of the resonance form of 12b
pyrid-2-yl ureas 3-6, 9, 10, 12, and 13. The syntheses
of these compounds are summarized in Schemes 2-4.
Since the corresponding isocyanate precursor of 3-6 is
unavailable commercially, we adopted a two-step syn-
thetic approach through a thiocarbamate intermediate.
Treatment of 2-aminopyridine (1) with S,S-dimethyl
dithiocarbonate (DMDTC) under basic conditions led to
thiocarbamate 2.12 Reaction of 2 with the corresponding
amines gave pyrid-2-yl ureas 3-6 in moderate yields.
Ureas 9-11 were prepared from the commercially
available isocyanate precursors 7 and 8.13 To understand
the charge effects on the bindings, we have further
converted 3 and 4 to positively charged 12 and 13,
is significant because the ureido nitrogen N(1) tends to
donate its lone pair electrons to the electron deficient
pyridinium ring. Consistent observation of alternating
C-C bond lengths on the pyridinium ring further sup-
ports this argument. Indeed, the bond lengths for C(2)-
(12) Leung, M.-k.; Lai, J .-L.; Lau, K.-H.; Yu, H.-h.; Hsiao, H.-J . J .
Org. Chem. 1996, 61, 4175.
(13) The compounds were purchased from Acros and were used
without further purification.
(14) Mayr, H.; Ofial, A. R.; Sauer, J .; Schmied, B. Eur. J . Org. Chem.
2000, 2013.
J . Org. Chem, Vol. 69, No. 6, 2004 1867

Chien et al.
TABLE 1. N-H Ch em ica l Sh ifts for 3-6 a n d 9-13 in
DMSO-d 6 a t Room Tem p er a tu r e
TABLE 2. Ch em ica l Sh ifts of th e Ur eid o N-H Sign a ls of
(E,Z)- a n d (Z,Z)-3, 4, 5, 9, 10, 11, a n d 12 in DMF -d 7 a t -70
°C
urea
δ (N-H)
urea
δ (N-H)
urea
NC-H
ND-H
NA-H and NB-H
3
4
5
6
9
10.56
10
11
12
13
9.34, 10.30
8.84, 9.08
9.56, 10.67
9.62, 11.00
9.45, 10.62
9.39, 10.48
3
4
12.6
12.7
13.0
12.3
12.2
14.7
13.8
10.4
10.5
10.5
10.2
10.1
11.2
11.0
9.7
9.7
10.1
9.8
9.9
10.6
10.9
10.65, (>12)a
9.97, 11.61
5
9.6
9.6
9.7
10.5
10.1
9
10
12
13
a
Estimated on the basis of the broad signal observed at δ 14.7
ppm in DMF-d7 at 0 °C.
C(3) and C(4)-C(5) were found to be 1.41 and 1.38 Å,
respectively, that is, longer than the bond lengths of 1.36
and 1.37 Å for C(3)-C(4) and C(5)-C(6), respectively.
While the ureido proton N(1)H is hydrogen bonded to
N(4), the second ureido proton on N(2) is thought to be
hydrogen bonded to the iodide anion. The distance
between the ureido proton N(2)H and I- was estimated
to be 2.78 Å. This NH‚ ‚ ‚I distance is consistent with the
literature values of two-center hydrogen bond lengths to
iodide that have been observed in the small molecular
crystal structures of nucleic acid components.15
Similar situations were observed for 13. The C-N bond
length of 1.373 Å for C(7)-N(2) is shorter than that of
1.406 Å for C(2)-N(1). Alternating C-C bond lengths of
the pyridinium ring are even more obvious in this case.
The bond lengths of 1.409 and 1.401 Å for C(7)-C(8) and
C(7)-C(11), respectively, are longer than the bond lengths
of 1.364 and 1.366 Å for C(8)-C(9) and C(10)-C(11),
respectively. These observations suggested that the
contribution of the resonance form of 13b is important.
Both of the ureido protons are thought to be hydrogen
bonded with the iodide anion.15 However, the distance
of 2.694 Å for N(2)H‚ ‚ ‚I is significantly shorter than that
of 2.931 Å for N(1)H‚ ‚ ‚I.
Th er m od yn a m ics of In tr a m olecu la r Hyd r ogen
Bon d in g a n d In ter m olecu la r Bin d in g w ith Cy-
tosin e. Intramolecular hydrogen bonding interaction was
F IGURE 3. 1H NMR spectra of 3 at different temperatures.
that only an average N-H proton signal was observed.
However, the exchange process was significantly slowed
at -70 °C and two conformers were clearly observed. On
the basis of the NMR assignments previously reported
in the literature,10a,b we assigned the signals at δ ) 12.6
and 10.4 ppm to the urea protons NC-H and ND-H of
the (E,Z) conformer, respectively. Since the NC-H is
intramolecularly hydrogen bonded to the pyridyl group,
it is supposed to be relatively downfield shifted. The
smaller signal at 9.7 ppm was assigned to the N-H
protons of the symmetrical (Z,Z) conformer. Perhaps due
to a steric hindrance, no evidence for the (E,E) conformer
was observed. The equilibrium constant Ki was evaluated
on the basis of the NMR integrations. To rule out the
influence arising from self-association of ureas on the
measurement of the equilibrium constants, the concen-
tration-dependence of the NH chemical shifts was exam-
ined. Indeed, identical NMR spectra were obtained in the
concentration range 0.008-0.014 M. These results imply
that self-association of urea in this concentration range
is less important. Similar assignments have been made
1
first examined by H NMR in DMSO-d6 at room temper-
ature, and the N-H resonance signals are summarized
in Table 1. While the N-H resonance signals of pyrid-
2-yl substituted ureas 3-6, 9-10, and 12-13 are rela-
tively downfield shifted to 9-12 ppm, 11 shows two N-H
singlets at 8.84 and 9.08 ppm. We tentatively attributed
the downfield shift phenomenon to being the result of
intramolecular hydrogen bonding interactions which
favor the formation of the (E,Z) conformers. Since 11 does
not contain a pyrid-2-yl group, we expected that steric
repulsion between the phenyl and pyrid-4-yl groups
would destabilize the (E,Z) conformer, giving the (Z,Z)
conformer as the predominant component. The equilib-
rium constants Ki, defined as [(E,Z)]/[(Z,Z)], were further
1
evaluated by H NMR in DMF-d7 at a low temperature,
and the δ values are listed in Table 2.11 As shown in
Figure 3, the conformational exchange between the E and
Z conformations of 3 at room temperature was so fast
(15) J effrey, G. A. An Introduction to Hydrogen Bonding; Oxford:
New York, 1997; p 77.
1868 J . Org. Chem., Vol. 69, No. 6, 2004

Substituent Effects on Pyrid-2-yl Ureas
TABLE 3. Equ ilibr iu m Con sta n ts a n d Th er m od yn a m ic
P a r a m eter s for th e P yr id -2-yl Ur ea s
urea
Kia
∆Hi° c
-2.3
∆Si° d
-8.8
KB (M-1
)
3
4
5
9
10
12
13
3.8 (1.9)b
1.7
30
590
1100
390
340
e
2.0
1.6
2.0
14.2
-0.8
-2.2
1.3
-10.6
1.0
1700
a
b
Ki ) [(E,Z)]/[(Z,Z)]. Due to the symmetry of 3, formation of
intramolecular hydrogen interaction is 2 times greater than that
of the others. c kcal/mol, estimated relative error <20%. cal/
d
mol‚K. e Unknown product was observed.
for 4-6, 9, 10, 12, and 13 (Table 2). Perhaps due to the
relatively low rotational energy barrier that leads to a
faster NsCdO bond rotation, the NsH proton signals
of 4-6, 9, and 10 were broad in comparison to those of
3, 12, and 13. Except for the case of 6, nevertheless, their
equilibrium constants could be reasonably estimated and
are summarized in Table 3. Among the pyrid-2-yl ureas
we studied, most of them have a Ki value of around 1-2,
indicating that there is only a small preference for the
(E,Z) form over the (Z,Z) form.
However, the Ki value of 14.2 ( 1.2 for 12 is unusually
high and is almost 1 order of magnitude larger than the
others. The results of the temperature-dependent experi-
ments revealed that the preference for the intramolecular
hydrogen bonding interaction arises from the entropy
factors. The (E,Z) conformation of 12 is indeed less
exothermic but entropically favored in comparison to the
cases of 3 and 13. The positive change in entropy for
intramolecular folding of 12 to give the (E,Z) conformer
is in sharp contrast to those of 3 and 13. Since there is a
positively charged methylpyridinium-2-yl group on 12,
solvation of this group by polar aprotic DMF molecules
should be significantly strong. Since this methylpyri-
dinium-2-yl center is adjacent to the ureido NC-H group,
intramolecular folding of 12 from the (Z,Z) form to the
(E,Z) form would partially occupy the solvation shell,
leading to a loss of the solvation enthalpy. This could
explain the observation of a less negative ∆H° value for
12. Moreover, releasing solvent molecules from the
solvation shell during intramolecular hydrogen bond
formation would lead to an increase of reaction entropy.
This kind of enthalpy-entropy compensation relationship
has been discussed in recent literature.16
F IGURE 4. 1H NMR spectra of 13 in the presence of different
equivalents of cytosine at -70 °C in DMF-d7.
between cytosine and 13. Although the assignments for
NA-H and NB-H are not immediately obvious, the
binding constants KB could still be unambiguously evalu-
ated on the basis of the trend of the N-H signal shifts.
On the other hand, the N-H signal intensities of the
(E,Z) isomer at 13.8 and 10.9 ppm progressively dropped
without any shift of the δ values. These observations are
consistent with our assumption that only (Z,Z)-13 would
bind with cytosine. However, binding between cytosine
and (Z,Z)-13 would shift the equilibrium toward the
(Z,Z)-13 side, reducing the amounts of (E,Z)-13 in solu-
tion.
As shown in Figure 5, the tendency of the δZ,Z values
follows the mathematical expression δZ,Z ) (δi + δfKB[C])/
(1 + KB[C]), where [C] is the concentration of free cytosine
in solution, δi is the initial chemical shift before addition
of cytosine, and δf is the final chemical shift in the
presence of a large excess of cytosine. The binding
constants KB were evaluated on the basis of a nonlinear
least-squares fitting of δZ,Z versus the concentration of
free cytosine, and they are summarized in Table 3.
Intermolecular complexation of pyridyl ureas with
1
cytosine has also been studied by H NMR at -70 °C. A
similar equilibrium system of model receptors for adenine
derivatives had been reported by Rebek.17 In each series
of studies, the concentration of cytosine was gradually
increased while the concentration of the target pyridyl
ureas was kept constant at around 0.01 M. Example
spectra of 13 are shown in Figure 4. Upon increasing the
amount of cytosine, the N-H chemical shifts δZ,Z of (Z,Z)-
13 gradually shifted from 10.1 and 10.9 ppm to 12.1 and
13.1 ppm, respectively, indicating complex formation
(16) (a) Williams, D. H.; O’Brien, D. P.; Bardsley, B. J . Am. Chem.
Soc. 2001, 123, 737. (b) Leung, M.-k.; Mandal, A. B.; Wang, C.-C.; Lee,
G.-H.; Peng, S. M.; Cheng, H.-L.; Her, G.-R.; Chao, I.; Lu, H.-F.; Sun,
Y.-C.; Shiao, M.-Y.; Chou, P. T. J . Am. Chem. Soc. 2002, 124, 4287.
(17) Tjivikua, T.; Deslongchamps, G.; Rebek, J ., J r. J . Am. Chem.
Soc. 1990, 112, 8408.
J . Org. Chem, Vol. 69, No. 6, 2004 1869

Chien et al.
lecular hydrogen bonding and cytosine complexation. The
N-methylpyridinium derivative 12 shows an unexpect-
edly strong tendency toward intramolecular hydrogen
bond interactions. On the other hand, the introduction
of an electron withdrawing substituent at the para
position of aryl pyrid-2-yl ureas particularly enhances the
intermolecular cytosine binding. Application of this con-
cept to the design of DNA binders is ongoing.
F IGURE 5. Plot of the N-H chemical shifts δZ,Z of (Z,Z)-13
vs [C], the concentration of free cytosine in solution.
Pyrid-2-yl ureas containing electron deficient or elec-
tron withdrawing groups, such as 5 or 13, show relatively
large binding constants KB of 1100 and 1700 M-1
,
respectively. In particular, 13 is the strongest receptor
for cytosine in the studied series, indicating the signifi-
cance of the charge effects on the binding. We tentatively
correlate this observation to the field-effect acidity en-
hancement of the NAsH by the attached electron with-
drawing aryl substituent and the partial positive-charge
delocalization onto the NA atom described in the discus-
sion of the X-ray crystallography. Although the acid-
base properties are far from linearly correlated to the
strengths of the hydrogen bonds, there are obvious
relationships between them.17 As the data in Table 2
show, the δ values of 10.1 and 10.9 ppm were found for
the NAsH protons of (Z,Z)-5 and (Z,Z)-13, respectively,
which are relatively more downfield than the average δ
value of 9.7 ( 0.1 ppm for the other ureido protons. These
imply that the NAsH group is a stronger hydrogen bond
donor than the normal ureido protons. According to these
results, we proposed that the NAsH of (Z,Z)-5 and (Z,Z)-
13 would be relatively acidic and therefore favorable for
hydrogen bonding with cytosine.18 Furthermore, the
partial positive charge delocalized onto the NA atom
through resonance from the attached pyridinium sub-
stituent of 13 would attract the partial negative charge
on the CdO group of cytosine, which is beneficial for the
hydrogen bond complex formation. Although we expected
that 12 would also be a strong cytosine binder, the
binding constant measurement of 12 with cytosine was
unfortunately hampered by formation of an unidentified
compound and could not be evaluated.
Exp er im en ta l Section
1H NMR Exp er im en ts for th e Deter m in a tion of Ki a n d
KB. The 1H NMR experiments were carried out in predried
DMF-d7 at low temperature. DMF-d7 was predried from
molecular sieves 4A and distilled. Equilibrium constants Ki
were measured at -70 °C on the basis of the NMR integration
of each isomer. To obtain the thermodynamic parameters ∆Hi°
and ∆Si° for 3, 12, and 13, temperature-dependent experi-
ments were carried out respectively at 203.25, 213.22, and
233.10 K. The concentration of the samples was set at 0.01
M. On the basis of the equation ∆Gi° ) -RT ln Ki ) ∆Hi° -
T∆Si°, the values of ∆Hi° and ∆Si° for 3, 12, and 13 were
evaluated from the linear regression of ln Ki versus 1/T.
To determine the cytosine binding constants KB, 1H NMR
titration experiments were carried out at -70 °C in DMF-d7.
The concentration of cytosine was increased gradually, while
the concentration of urea was kept constant. The binding
constants were evaluated on the basis of the nonlinear
regression method shown in the Supporting Information. The
binding constants were doubly checked by the integration
approach. The data were also shown in the Supporting
Information. The values from the two approaches are consis-
tent with each other.
S-Meth yl (N-(P yr id -2-yl)th ioca r ba m a te (2).20 To a solu-
tion of 2-aminopyridine (4.11 g, 43.7 mmol) and 1,1,1,3,3,3-
hexamethyldisilazane (7.24 g, 44.9 mmol) in THF (35 mL)
under N2 at -78 °C was added n-butyllithium (1.6 M in
hexane, 87.2 mmol). After addition, the solution was stirred
for 30 min, and a solution of DMDTC (5.45 g, 44.6 mmol) in
THF (10 mL) was added. The reaction mixture was further
stirred for 20 h, and during the course of this, the temperature
was gradually raised to room temperature. The reaction was
quenched by addition of water. The product was collected by
extraction with CH2Cl2 for three times. The organic extracts
were collected, dried over anhydrous MgSO4, concentrated, and
recrystallized from hexane-CH2Cl2 to give colorless crystals
(5.51 g, 32.8 mmol, 47%). mp 116-118 °C (lit.17 113-114,
EtOH); 1H NMR (400 MHz, DMSO-d6) δ 10.90 (s, 1H), 8.27
(m, 1H), 7.83 (d, J ) 8 Hz, 1H), 7.76 (m, 1H), 7.07 (m, 1H),
2.27 (s, 3H); 13C NMR (75 MHz, CDCl3) δ 167.0, 151.8, 147.8,
138.7, 119.2, 114.1, 12.3; IR (KBr) (cm-1) 3448 (NH), 1695 (Cd
O); MS (EI, 70 eV) m/e 168 (M+, 15), 153 (65), 121 (53), 78
(100); HRMS (EI, 70 eV) calcd for C7H8N2OS 168.0357, obsd
168.0363. Anal. Calcd for C7H8N2OS: C, 49.98; H, 4.79; N,
16.65. Found: C, 49.82; H, 4.73; N, 16.68.
The KB value of 30 M-1 for 3 is particularly small in
comparison to the others in the series. We tentatively
attribute this phenomenon to the secondary electrostatic
repulsion between the pyridyl nitrogen and the carbonyl
group of cytosine in 14. The secondary electrostatic
repulsion model was proposed by J orgenson and later on
quantified by Schneider.19 Although one may suggest that
rotation of the pyridyl group away from the cytosine
would lead to less repulsion, as shown in 15, this will
create another electrostatic repulsion between the pyridyl
nitrogen and the ureyleno carbonyl group.
In summary, we report herein the unexpected sub-
stituent effects on aryl pyrid-2-yl ureas toward intramo-
(19) (a) Pranata, J .; Wierschke, S. G.; J orgensen, W. L. J . Am. Chem.
Soc. 1991, 113, 2810. (b) J orgensen, W. L.; Pranata, J . J . Am. Chem.
Soc. 1990, 112, 2008. (c) Sartorius, J .; Schneider, H.-J . Chem.sEur.
J . 1996, 2, 1446.
(20) Gilbert, G.; Wetstein, H. U.S. Patent 3284460, 1966; Chem.
Abstr. 1968, 49462.
(18) For reviews of the relationship between hydrogen bond strength
and acid-base properties, see: (a) Pogorelyi, V. K.; Vishnyakova, T.
B. Russ. Chem. Rev. 1984, 53, 1154. (b) Epshtein, L. M. Russ. Chem.
Rev. 1979, 48, 854.
1870 J . Org. Chem., Vol. 69, No. 6, 2004

Substituent Effects on Pyrid-2-yl Ureas
N,N′-Di(p yr id -2-yl)u r ea (3).10b A solution of 2-aminopy-
ridine (3.60 g, 38.6 mmol) and 2 (5.00 g, 29.7 mmol) in THF
(12 mL) was refluxed for 24 h. The solvent was then removed
under reduced pressure by using a rotary evaporator. The
crude solid was then recrystallized from CHCl3 to give 3 as
colorless crystals (4.00 g, 8.7 mmol, 62%). mp 174-176 °C; 1H
NMR (400 MHz, DMSO-d6) δ 10.56 (bs, 2H), 8.27-8.29 (m,
2H), 7.72-7.76 (m, 2H), 7.65-7.71 (m, 2H), 7.02-7.05 (m, 2H);
13C NMR (400 MHz, DMSO-d6) δ 152.4, 151.9, 147.3, 138.5,
118.2, 112.4; IR (KBr) (cm-1) 3226 (NH), 1701 (CdO); FAB
(NBA) 215.1 (M+ + H); HRMS (FAB) calcd for C11H10N4O
214.0855 (M+ + H), obsd 214.0978.
was added MeI (0.7 mL (CH3I), 1.6 g, 11 mmol). After the
mixture was stirred for 2 h, a yellowish precipitate formed.
The reaction was monitored by 1H NMR and finished after 11
h. The product was precipitated by addition of ethyl acetate,
collected by suction filtration, washed with distilled water, and
dried under vacuum to give 13 (0.4 g, 1 mmol, 33%) as slightly
yellowish crystals. mp 218-220 °C; 1H NMR (400 MHz,
DMSO-d6) δ 11.61 (s, 1H), 9.98 (s, 1H), 8.66 (d, J ) 8 Hz, 2H),
8.33-8.35 (m, 1H), 8.04 (d, J ) 8 Hz, 2H), 7.82-7.85 (m, 1H),
7.59 (d, J ) 8 Hz, 1H), 7.11-7.16 (m, 1H), 4.14 (s, 3H); 13C
NMR (400 MHz, DMSO-d6) δ 151.9, 151.5, 151.3, 147.4, 145.6,
139.1, 119.0, 114.2, 112.5, 46.1; IR (KBr) (cm-1) 3238 (NH),
1729 (CdO); FAB (NBA) 229.1 (M+); HRMS (FAB) calcd for
N-(P yr id -4-yl)-N′-(p yr id -2-yl)u r ea (4).10b A solution of
4-aminopyridine (0.73 g, 7.8 mmol) and 2 (1.00 g, 5.90 mmol)
in THF (2.7 mL) was refluxed for 19 h. The solvent was
removed under reduced pressure by using a rotary evapora-
tor. The crude solid collected was then recrystallized from
methanol to give 4 as colorless crystals (0.18 g, 0.8 mmol, 14%).
C
12H13N4O+ 229.1089 (M+), obsd 229.1087.
N-P h en yl-N′-(pyr id-2-yl)u r ea (9).10f To a solution of 2-ami-
nopyridine (0.95 g, 10.1 mmol) in CaH2 dried 1,4-dioxane under
nitrogen was added phenylisocyanate (1.5 mL, 13.7 mmol).
After being refluxed for 1 h, the solution was cooled to room
temperature and white precipitate formed. The precipitate was
collected by suction filtration and recrystallized from EtOH
to give 9 as white solid (0.85 g, 4.0 mmol, 39%). mp 201-204
°C; 1H NMR (400 MHz, DMSO-d6) δ 10.48 (s, 1H), 9.40 (s, 1H),
8.25-8.27 (m, 1H), 7.770-7.76 (m, 1H), 7.47-7.52 (m, 3H),
7.28-7.32 (m, 2H), 6.97-7.03 (m, 2H); 13C NMR (400 MHz,
DMSO-d6) δ 152.9, 152.2, 146.9, 139.0, 138.5, 128.9, 122.5,
118.8, 117.5, 111.9; IR (KBr) (cm-1) 3224 (NH), 1691 (CdO);
FAB (NBA) 214.1 (M+ + H); HRMS (FAB) calcd for C12H11N3O
214.0980 (M+ + H), obsd 214.0983.
1
mp 192-194 °C; H NMR (400 MHz, DMSO-d6) δ 10.68 (bs,
1H), 9.56 (s, 1H), 8.38 (d, J ) 5 Hz, 2H), 8.28-8.29 (m, 1H),
7.76-7.78 (m, 1H), 7.55 (d, J ) 8 Hz, 1H), 7.50 (d, J ) 5 Hz,
2H), 7.03-7.05 (m, 1H); 13C NMR (400 MHz, DMSO-d6) δ
152.3, 151.9, 150.3, 147.1, 145.8, 138.7, 118.1, 112.8, 112.1;
IR (KBr) (cm-1) 3230 (NH), 1704 (CdO); FAB (NBA) 215.1 (M+
+ H); HRMS (FAB) calcd for C11H11N4O 215.0933 (M+ + H),
obsd 215.0930.
N-(4-Nitr op h en yl)-N′-(p yr id -2-yl)u r ea (5).8d A solution
of 4-nitroaniline (1.07 g, 7.7 mmol) and 2 (1.01 g, 6.0 mmol)
in THF (2.6 mL) was refluxed for 24 h. Rotary evaporation of
the solvent gave a crude solid that was further recrystallized
from EtOAc to give 5 as a slightly brownish solid (0.59 g, 2.3
N-(4-Meth oxyp h en yl)-N′-(p yr id -2-yl)u r ea (10).22 To a
solution of 2-aminopyridine (0.60 g, 6.4 mmol) in THF (14 mL)
was added 4-methoxyphenylisocyanate (1.01 mL, 7.7 mmol).
After being refluxed for 1 h, the solution was cooled to room
temperature. The white precipitate formed was collected by
suction filtration. Recrystallization of the precipitate from
EtOH-EtOAc gave 10 as colorless needles (1.24 g, 5.1 mmol,
80%). mp 213-215 °C (lit.19 206-207); 1H NMR (400 MHz,
DMSO-d6) δ 10.37 (s, 1H), 9.35 (s, 1H), 8.24-8.26 (m, 1H),
7.67-7.73 (t, J ) 7 Hz, 1H), 7.38-7.43 (m, 3H), 6.94-6.99 (m,
1H), 6.87 (d, J ) 8 Hz, 2H), 3.71 (s, 3H); 13C NMR (400 MHz,
DMSO-d6) δ 154.9, 153.0, 152.3, 146.8, 138.5, 132.0, 120.6,
117.3, 114.1, 111.8, 55.2; IR (KBr) (cm-1) 3227 (NH), 1697 (Cd
O); FAB (NBA) 244.1 (M+ + H); HRMS (FAB) calcd for
1
mmol, 38%). mp 246-248 °C; H NMR (400 MHz, DMSO-d6)
δ 11.01 (bs, 1H), 9.62 (bs, 1H), 8.28-8.30 (m, 1H), 8.19 (d, J )
8 Hz, 2H), 7.74-7.78 (m, 3H), 7.52 (d, J ) 8 Hz, 1H), 7.02-
7.05 (m, 1H); 13C NMR (400 MHz, DMSO-d6) δ 152.8, 152.3,
147.5, 146.0, 142.0, 139.2, 125.6, 118.7, 118.6, 112.6; IR (KBr)
(cm-1) 3218 (NH), 1705 (CdO); FAB (NBA) 259.1 (M+ + H);
HRMS (FAB) calcd for C12H11N4O3 259.0831 (M+ + H), obsd
259.0837.
N-(4-Ch lor op h en yl)-N′-(p yr id -2-yl)u r ea (6).21 A solution
of 4-chloroaniline (0.98 g, 7.7 mmol) and 2 (1.01 g, 6.0 mmol)
in THF (2.6 mL) was refluxed for 36 h. Rotary evaporation of
the solvent gave a crude solid that was further recrystallized
from EtOAc to give 6 as colorless needles (0.70 g, 2.8 mmol,
47%). mp 205-207 °C; 1H NMR (400 MHz, DMSO-d6) δ 10.62
(s, 1H), 9.45 (s, 1H), 8.25-8.27 (m, 1H), 7.73-7.77 (m, 1H),
7.55 (d, J ) 8 Hz, 2H), 7.46 (d, J ) 8 Hz, 1H), 7.34 (d, J ) 8
Hz, 2H), 6.98-7.02 (m, 1H); 13C NMR (400 MHz, DMSO-d6) δ
153.2, 152.6, 147.4, 139.1, 138.5, 129.2, 126.5, 120.8, 118.1,
112.4; IR (KBr) (cm-1) 3219 (NH), 1696 (CdO); FAB (NBA)
248.0 (M+ + H); HRMS (FAB) calcd for C12H11ClN3O 248.0591
(M+ + H), obsd 248.0599.
C
13H13N3O2 244.1086 (M+ + H), obsd 244.1083.
N-P h en yl-N′-(p yr id -4-yl)u r ea (11).10f To a solution of
4-aminopyridine (4.90 g, 52.1 mmol) in THF (150 mL) was
added phenylisocyanate (5.77 mL, 52.6 mmol). After being
refluxed for 19 h, the solution was concentrated under reduced
pressure to give a crude solid. Recrystallization of the crude
solid from methanol gave 11 as a white solid (2.53 g, 11.9
1
mmol, 22%). mp 180-182 °C; H NMR (400 MHz, DMSO-d6)
δ 9.08 (s, 1H), 8.84 (s, 1H), 8.33-8.35 (m, 2H), 7.42-7.47 (m,
4H), 7.29 (t, J ) 8 Hz, 2H), 7.00 (t, J ) 8 Hz, 1H); 13C NMR
(400 MHz, DMSO-d6) δ 152.1, 150.1, 146.5, 139.1, 128.8, 122.4,
118.5, 112.2; IR (KBr) (cm-1) 3345 (NH), 1706 (CdO); FAB
(NBA) 214.1 (M+ + H); HRMS (FAB) calcd for C12H11N3O
214.0980 (M+ + H), obsd 214.0983.
1-Meth yl-2-(3-(pyr id-2-yl)u r eido)pyr idin iu m Iodide (12).
To a solution of 3 (0.50 g, 2.3 mmol) in DMSO (2.6 mL) was
added MeI (0.44 mL, 0.99 g, 7.0 mmol). After the mixture was
stirred for 2 h, a yellowish precipitate formed. The reaction
was monitored by 1H NMR and finished after 7 h. The product
was precipitated by addition of ethyl acetate, collected by
suction filtration, washed with distilled water, and dried under
vacuum to give 12 (0.35 g, 1.0 mmol, 42%) as colorless crystals.
Ack n ow led gm en t. We thank the National Science
Council of Republic of China for the financial support
(NSC 91-2113-M-002-024).
1
mp 187-190 °C; H NMR (400 MHz, DMSO-d6) δ 10.66 (bs,
1H), 8.73 (d, J ) 6 Hz, 1H), 8.65 (d, J ) 8 Hz, 1H), 8.41-8.43
(m, 1H), 8.37 (t, J ) 8 Hz, 1H), 7.88-7.92 (m, 1H), 7.52-7.58
(bt, 1H), 7.27-7.33 (bs, 1H), 7.16-7.18 (m, 1H), 4.22 (s, 3H);
13C NMR (400 MHz, DMSO-d6) δ 151.6, 151.0, 149.3, 145.9,
144.8, 143.6, 140.2, 119.0, 118.5, 117.9, 112.1, 43.9; IR (KBr)
(cm-1) 3145 (NH), 1734 (CdO); FAB (NBA) 229.1 (M+); HRMS
(FAB) calcd for C12H13N4O+ 229.1089 (M+), obsd 229.1090.
1-Meth yl-4-(3-(pyr id-2-yl)u r eido)pyr idin iu m Iodide (13).
To a solution of 4 (0.8 g, 4 mmol) in DMSO (4 mL) at 30 °C
Su p p or tin g In for m a tion Ava ila ble: Evaluation of the
binding constant KB, figures showing the binding experiments
of ureas 3, 4, 5, 9, 10, and 13 with various amounts of cytosine,
and CIF files for 12 and 13. This material is available free of
charge via the Internet at http://pubs.acs.org.
J O0355808
(21) Le Magueres, P.; Ouahab, L.; Hocquet, A.; Fournier, J . Acta
Crystallogr. 1994, C50, 1507.
(22) Novikov, E. G. Khim. Geterotsikl. Soedin., Sb. (in Russian) 1968,
1, 115; Chem. Abstr. 1970, 3776.
J . Org. Chem, Vol. 69, No. 6, 2004 1871