The G-C DNA base hybrid: Synthesis, self-organization and structural analysis

Article abstract of DOI:10.1021/jo990719t

The guanine-cytosine base hybrid I is synthesized in five steps from the malononitrile dimer. One face of the molecule possesses the cytosine AAD hydrogen bonding code and the other the guanine DDA code. The expression of this information leads to the self-organization of six molecules of I into a hexagonal supermacrocycle in the solid state through the formation of 18 strong hydrogen bonds. This is the first structurally characterized example of a synthetic hexagonal assembly where the molecular program is unambiguous and all of the information required for exclusive rosette formation is contained within hydrogen bonding codes. 1 crystallizes in the very rare, high-symmetry cubic space group Ia3d, with 96 molecules in the unit cell. The crystal is highly solvated and only ca. 35% occupied by molecules of 1, with a criss-crossed network of channel voids generated by the overlapping of 1₆ hexamers.

Full text of DOI:10.1021/jo990719t

J . Org. Chem. 1999, 64, 8479-8484
8479
Th e G-C DNA Ba se Hybr id : Syn th esis, Self-Or ga n iza tion a n d
Str u ctu r a l An a lysis
Mark Mascal,*,† Nicholas M. Hext,† Ralf Warmuth,† J ames R. Arnall-Culliford,†
Madeleine H. Moore,‡ and J ohan P. Turkenburg‡
Department of Chemistry, University of Nottingham, Nottingham, UK NG7 2RD, U.K., and
Department of Chemistry, University of York, Heslington, York, UK YO1 5DD, U.K.
Received April 28, 1999
The guanine-cytosine base hybrid 1 is synthesized in five steps from the malononitrile dimer.
One face of the molecule possesses the cytosine AAD hydrogen bonding code and the other the
guanine DDA code. The expression of this information leads to the self-organization of six molecules
of 1 into a hexagonal supermacrocycle in the solid state through the formation of 18 strong hydrogen
bonds. This is the first structurally characterized example of a synthetic hexagonal assembly where
the molecular program is unambiguous and all of the information required for exclusive rosette
formation is contained within hydrogen bonding codes. 1 crystallizes in the very rare, high-symmetry
cubic space group Ia3hd, with 96 molecules in the unit cell. The crystal is highly solvated and only
ca. 35% occupied by molecules of 1, with a criss-crossed network of channel voids generated by the
overlapping of 16 hexamers.
In tr od u ction
Resu lts a n d Discu ssion
Our initial synthetic approach was built up around the
easy availability of 2-bromo-3-cyano-4,6-diaminopyridine
2,6 which is derived in one step from malononitrile and
already possesses most of the carbon-nitrogen frame-
work of 1. Reaction of 2 with the NH2O- equivalent
acetone oxime7 (Scheme 2) gave the oximino ether 3 in
60% yield, which on hydrolysis produced the isoxazole
4. This material then underwent smooth hydrogenolysis
to the amidinopyridone 5. Attempts, however, to obtain
a pyrido[4,3-d]pyrimidine system by reaction of 5 with
phosgene or equivalents (diethyl carbonate, ethyl chloro-
formate, trichloromethyl chloroformate) failed under a
range of conditions, possibly due to its limited solubility.
The difficulties inherent in this route led to a rework-
ing of the synthesis, in which a solubilizing group was
featured and which avoided the intermediacy of an
amidine. Thus, the commercially available (or readily
prepared)8 malononitrile dimer 6 was alkylated by reac-
tion with heptyl bromide in the presence of Hu¨nigs base
in 71% yield (Scheme 3). The product 7 could be cyclized
with hydrogen bromide to the corresponding bromo-
pyridine 8 in 90% yield and the requisite oxygen func-
tionality introduced by nucleophilic displacement with
methoxide. However, direct cyclization of 7 with meth-
oxide9 was found to be more convenient, even though it
gave a mixture of 9 (69%) and its regioisomer 10 (19%).
The more nucleophilic 6-amino group of compound 9 had
then to be protected in order to elaborate at the 4-nitro-
gen. Considerable trial-and-error at this point eventually
led to the preparation of a methyl carbamate 11 by
treatment the dianion of 9 with dimethyl carbonate. The
key transformation leading to the bicyclic system 12 was
originally accomplished by reaction of 11 with chlorosul-
The pyridopyrimidine 1 is a DNA base hybrid: It
incorporates the complementary hydrogen bonding codes
of both cytosine (AAD) and guanine (DDA) in the same
molecule. Situated at 120° angles to each other, these
codes define a molecular program that drives the merger
of six molecules of 1 into a hexagonal supermacrocycle
(Scheme 1).1 This was the first example of a structurally
characterized, nonnatural molecular aggregate whose
subunits possessed information of a standard sufficient
to unambiguously dictate this particular mode of as-
sembly.2 Furthermore, the energetics of the association
process were maximized by the effectiveness of the
nonsymmetric H-bond pattern,3 such that self-organiza-
tion could take place in polar solvents (DMF, DMSO),
from which crystals of 1 grew. Relevant to this point was
concurrent work by Lehn and co-workers,4 whose study
of a closely related molecule provided direct evidence
using vapor-pressure osmometry that this hexameric
state of aggregation also exists in solution. Later work
employing size-exclusion chromatography on yet another
similar molecule comes to the same conclusion.5 We now
report the details of the synthesis and structure of 1.
* To whom correspondence should be addressed. Tel: +115-951-
3541. Fax: +115-951-3564. E-mail: mark.mascal@nottingham.ac.uk.
† University of Nottingham.
‡ University of York.
(1) Preliminary report plus background discussion: Mascal, M.;
Hext, N. M.; Warmuth, R.; Moore, M. H.; Turkenburg, J . P. Angew.
Chem., Int. Ed. Engl. 1996, 35, 2204.
(2) The melamine barbiturate system of Whitesides et al. uses
centrosymmetric H-bonding codes, which gives rise to polymeric
assemblies as well as rosettes: (a) Zerkowski, J . A.; Whitesides, G. M.
J . Am. Chem. Soc. 1994, 116, 4298. (b) Zerkowski, J . A.; Mathias, J .
P.; Whitesides, G. M. J . Am. Chem. Soc. 1994, 116, 4305. (c) Mathias,
J . P.; Simanek, E. E.; Zerkowski, J . A.; Seto, C. T.; Whitesides, G. M.
J . Am. Chem. Soc. 1994, 116, 4316.
(3) Pranata, J .; Wierschke, S. G.; J orgensen, W. L. J . Am. Chem.
Soc. 1991, 113, 2810.
(4) Marsh, A.; Silvestri, M.; Lehn, J .-M. Chem. Commun. 1996, 1527.
(5) Kolotuchin, S. K.; Zimmerman, S. C. J . Am. Chem. Soc. 1998,
120, 9092.
(6) Carboni, R. A.; Coffman, D. D.; Howard, E. G. J . Am. Chem. Soc.
1958, 80, 2838.
(7) Shutske, G. M.; Kapples, K. J . J . Heterocycl. Chem. 1989, 26,
1293.
(8) Mittelbach, M. Monatsh. Chem. 1985, 116, 689.
(9) J unek, H.; Uray, G.; Kotzent, A. Monatsh. Chem. 1983, 114, 973.
10.1021/jo990719t CCC: $18.00 © 1999 American Chemical Society
Published on Web 11/12/1999

8480 J . Org. Chem., Vol. 64, No. 23, 1999
Mascal et al.
Sch em e 1
Sch em e 2
Sch em e 3
fonyl isocyanate followed by aqueous workup in a dis-
appointing 15% yield.1 We have now improved the
conversion to 12 to a more satisfactory 47% by sequential
addition of phosgene, ammonia, and methoxide to 11.
Compound 12 was finally treated with TMS-iodide to
simultaneously demask both the 6-amino group and the
latent carbonyl function, and the target material 1 was
isolated in 73% yield.
Compound 1 was practically insoluble in alcohols,
ethers, and halogenated solvents but readily went into
dimethyl formamide and dimethyl sulfoxide. Preparation
of dilute solutions of 1 at slightly elevated temperatures
in either of these solvents, or mixtures thereof, resulted
after several hours in the deposition of large, clear
crystals of cubic habit that showed no extinction of plane-
polarized light. Despite the apparent quality of the
crystals, initial attempts to characterize 1 by X-ray
diffraction were unsuccessful, and it was only when more
powerful techniques were applied that the crystals

The G-C DNA Base Hybrid
J . Org. Chem., Vol. 64, No. 23, 1999 8481
F igu r e 1. Oblique view of the hexagonal packing of 1 in the crystal.
yielded to analysis. Because crystals of 1 rapidly desol-
vated on exposure to air and did not withstand freezing,
data had to be collected at room temperature on samples
mounted in sealed capillaries. Reflections could not be
resolved using a basic, sequential crystallographic pro-
tocol. The use, however, of an area detector and rotating
anode Cu KR radiation source did give a good dataset to
the maximum resolution available (1.66 Å), which,
although not sufficient to solve the structure, indicated
a very large unit cell with a ) 47 Å and V >100 000 A3.
A solution was ultimately derived from data collected
using a synchrotron radiation source, and the result
confirmed the predicted hexagonal mode of assembly
(Figure 1). Six molecules of 1 thus converge into a ring
fixed by 18 strong H-bonds as dictated by the G-C
pairing codes, with distances O‚‚‚N (outer) 2.80, N‚‚‚N
2.91, and O‚‚‚N (inner) 2.91 Å. The molecule crystallizes
in the very rare cubic space group Ia3hd (number 230), in
which only two other organic structures have been
reported.10 There are 96 molecules of 1 in the unit cell,
with a single molecule of 1 in the asymmetric unit and
96-fold symmetry in the crystal.
An additional feature of the structure is that the
hexamers coincide with one another to describe channels
that extend through the crystal parallel to the body
diagonals. The view of the unit cell down [111] in Figure
2, which shows how each 10.5 Å channel is surrounded
by six triangular voids in a Star of David type arrange-
ment, about the periphery of which another six channels
occur. Although these features can be clearly identified
in Figure 2, distinguishing individual hexamers is com-
plicated by the fact that each is rotated 24° relative to
the one above it. The alkyl chains of neighboring subunits
protrude 2.7 Å above and below the hexamer plane in
an alternating pattern of 3h symmetry. The mobility of
these groups is marked and increases progressively with
distance from the rigid aromatic core, such that discrete
positions for the two terminal carbons could not be found.
The 16 units do not “stack” in the traditional sense but
are separated by about 20 Å along the channel axis. The
calculated density of the crystal is remarkably low (0.479
g cm-3), indicating that ca. 65% of the cell is “unoccupied”.
Since the presence of only 0.7 solvent molecules (DMSO
in this case) per molecule of 1 could be modeled on the
(10) (a) Simonov, Y. A.; Malinovskii, S. T.; Bologa, O. A.; Zavodnik,
V. E.; Andrianov, V. I.; Shibanova, T. A. Kristallografiya 1983, 28, 682.
(b) Lebuis, A.-M.; Young, J . M. C.; Beauchamp, A. Can. J . Chem. 1993,
71, 2070.

8482 J . Org. Chem., Vol. 64, No. 23, 1999
Mascal et al.
F igu r e 2. A view of the cell of 1 down a body diagonal.
data, the remainder of the space is apparently filled by
highly disordered (or liquid) solvent. The vacancies in the
structure raise the intriguing prospect of cocrystallizing
1 with species complementary to the channel voids,
particularly polymeric materials (peptides, saccharides),
which should act to reinforce the assembly and thereby
also improve the physical integrity of the crystals.
In conclusion, the adaptation of reciprocal DNA-base
codes in G-C hybrid molecule 1 to self-organization
processes leads to the first structurally characterized
example of an unambiguous hexagonal mode of assembly.
The robustness of the assembly provides an unparalleled
means of creating hexagonal order on the molecular scale.
Current efforts on our part in this area include the
organization of sterically demanding substituents in the
periphery of 16 in an attempt to force the subunits from
planarity. This would introduce a “screw defect” into the
ring resulting in an H-bonded polymer with helical
secondary structure. The previously mentioned issue of
the host properties of the zeolite-like lattice of 1 is also
under investigation, and progress along these lines will
be reported in due course.
Exp er im en ta l Section
3-Cya n o-4,6-d ia m in o-2-isop r op ylid in ea m in ooxyp yr i-
d in e (3). Potassium tert-butoxide (1.21 g, 10.8 mmol) was
added to a solution of acetone oxime (765 mg, 10.5 mmol) in
dry DMF (20 mL) under nitrogen. The suspension was stirred
for 1 h at room temperature, and then 2-bromo-3-cyano-4,6-
diaminopyridine 2 (2.13 g, 10.0 mmol) in dry DMF (10 mL)
was added and the resulting red-orange solution stirred for
20 h at 60 °C. Saturated aqueous NaHCO3 (20 mL) and water
(20 mL) were added, and the solution was then neutralized
with 2 M HCl. After extraction with chloroform (×4), the
combined organic layer was dried over MgSO4 and the solvent
evaporated. The residue was chromatographed (3:7 acetone/
CH2Cl2) to give starting material 2 (420 mg) and product 3
(1.24 g, 60%) as pale yellow solid: 1H NMR (250 MHz; DMSO-
d6) δ 1.94 (3 H, s), 1.98 (3 H, s), 5.37 (1 H, s), 6.27 (2 H, br s),
6.39 (2 H, br s); 13C NMR (100 MHz; DMSO-d6) δ 16.1, 21.2,
67.3, 83.6, 158.1, 160.7, 161.1, 165.5. Anal. Calcd for
C9H11N5O: C, 52.7; H, 5.4; N, 34.1. Found: C, 52.5; H, 5.6; N,
34.2.
Isoxa zolo[5,4-b]p yr id in e-3,4,6-tr ia m in e (4). Compound
3 (2.90 g, 14.1 mmol) was added to 0.5 M aqueous NaOH (200
mL), and the suspension was heated at 90 °C for 30 h under
nitrogen. The reaction mixture was neutralized with 6 M HCl,

The G-C DNA Base Hybrid
J . Org. Chem., Vol. 64, No. 23, 1999 8483
saturated with NaCl, and extracted with 1:1 ethyl acetate/
methanol (×3). The aqueous layer was evaporated and the
residue triturated with hot 1:1 acetone/methanol. The organic
extracts were combined, the solvent was evaporated, and the
crude product was preabsorbed onto silica gel. Chromatogra-
phy (12:1 f 3:1 EtOAc/MeOH) gave 3-cyano-4,6-diamino-2-
pyridone (710 mg, 33%)11 and the product 4 (670 mg, 29%) as
a pale yellow solid: 1H NMR (250 MHz; DMSO-d6) δ 5.35 (1
H, s), 5.81 (2 H, s), 5.96 (2 H, s), 6.26 (2 H, s); 13C NMR (67.8
MHz; DMSO-d6) δ 84.8, 86.1, 151.1, 157.8, 161.7, 172.1. Anal.
Calcd for C6H7N5O: C, 43.6; H, 4.3; N, 42.4. Found: C, 43.5;
H, 4.5; N, 42.6.
4,6-Dia m in o-2-p yr id on e-3-ca r boxa m id in e (5). To a solu-
tion of compound 4 (100 mg, 0.60 mmol) in methanol (20 mL)
was added 10% Pd on activated charcoal (40 mg). The mixture
was degassed by flushing with hydrogen (×3) and stirred at
room temperature over hydrogen for 24 h. The reaction was
filtered and the solvent evaporated to give 5 (94 mg, 93%):
1H NMR (250 MHz; DMSO-d6) δ 4.96 (1 H, s), 6.42 (2 H, br s),
8.01 (6 H, br s); 13C NMR (67.8 MHz; DMSO-d6) δ 78.2, 84.4,
152.2, 160.6, 164.1, 164.4; m/z (CI/NH3) 168 (M + H, 100).
SO4) and the solvent evaporated to give a white solid. Chro-
matography (0 f 40% ether in hexanes) provided, in order of
elution, compound 10 (0.104 g, 19%) and compound 9 (0.370
g, 69%).
9: mp 62.5-63.5 °C (from EtOAc/hexanes); 1H NMR (400
MHz; CDCl3) δ 0.88 (3 H, t, J 6.9), 1.15-1.40 (8 H, br m), 1.48
(2 H, quintet, J 7.7), 2.25 (2 H, t, J 7.8), 3.87 (3 H, s), 4.56 (2
H, br s), 4.62 (2 H, br s); 13C NMR (100 MHz; CDCl3) δ 14.0,
22.6, 24.7, 27.3, 29.2, 29.8, 31.8, 53.5, 71.7, 94.6, 116.5, 155.1,
157.1, 163.8. Anal. Calcd for C14H22N4O: C, 64.1; H, 8.5; N,
21.4. Found: C, 64.1; H, 8.6; N, 21.5.
10: mp 134.5-135 °C (from EtOAc/hexanes); 1H NMR (400
MHz; CDCl3) δ 0.88 (3 H, t, J 7.0), 1.20-1.32 (8 H, br m), 1.40
(2 H, m), 2.33 (2 H, t, J 7.6), 3.83 (3 H, s), 4.53 (2 H, br s), 4.76
(2 H, br s); 13C NMR (100 MHz; CDCl3) δ 14.1, 22.6, 23.0, 28.2,
29.2, 29.5, 31.8, 53.6, 70.7, 96.5, 117.1, 154.4, 157.9, 164.0.
Anal. Calcd for C14H22N4O: C, 64.1; H, 8.5; N, 21.4. Found:
C, 64.3; H, 8.7; N, 21.3.
4-Am in o-3-cya n o-5-h ep tyl-2-m eth oxy-6-[(m eth oxyca r -
bon yl)a m in o]p yr id in e (11). tert-Butyllithium (1.7 M in
pentanes, 4.0 mL, 6.8 mmol) was added dropwise to a stirred
suspension of 9 (0.786 g, 3.00 mmol) in DME (40 mL) at -78
°C, during which time the reaction became homogeneous. The
mixture was allowed to warm to room temperature over a
period of 1 h, and dimethyl carbonate (5.0 mL, 5.3 g, 59 mmol)
was added. The reaction was then stirred at room temperature
for 19 h. All volatiles were removed under reduced pressure,
aqueous NaHCO3 (2%, 50 mL) was added, and the mixture
was extracted with dichloromethane (×5). The combined
organic extract was dried (MgSO4) and the solvent evaporated
to give a pale yellow solid. Chromatography (0 f 50% ethyl
acetate in hexanes) gave 11 (0.829 g, 86%) as a white solid:
2-Am in o-1,1,3-t r icya n o-1-d ecen e (7). Diisopropylethyl-
amine (5.5 mL, 4.1 g, 31.6 mmol) was added to a solution of
2-amino-1,1,3-tricyanopropene 68 (1.995 g, 15.1 mmol) in DME
(50 mL) and the solution stirred at room temperature for 40
min. 1-Bromoheptane (10.0 mL, 11.4 g, 63.6 mmol) and
tetrabutylammonium iodide (0.33 g, 0.89 mmol) were added,
and the suspension was heated at reflux for 110 h with light
excluded. The mixture was cooled to room temperature, and
the precipitated ammonium salt was filtered off and washed
with ethyl acetate (×5). The solvent was evaporated and the
residue partitioned between hydrochloric acid (0.4 M, 100 mL)
and dichloromethane (50 mL). The aqueous layer was ex-
tracted with additional dichloromethane (×4), the combined
organic extract dried (MgSO4), and the solvent evaporated to
give a black oil. Chromatography (0 f 100% ether in hexanes)
gave 7 (2.459 g, 71%) as a pale orange solid: mp 70.5-71.5
°C (from EtOH/H2O); 1H NMR (400 MHz; CDCl3) δ 0.90 (3 H,
t, J 6.9), 1.29-1.41 (8 H, m), 1.50-1.61 (2 H, m), 1.95-2.02 (2
1
mp 118-121 °C; H NMR (400 MHz; CDCl3) δ 0.89 (3 H, t, J
7.0), 1.28-1.32 (8 H, m), 1.48 (2 H, quintet, J 7.3), 2.39 (2 H,
t, J 7.9), 3.79 (3 H, s), 3.94 (3 H, s), 4.92 (2 H, br s), 6.62 (1 H,
br s); 13C NMR (100 MHz; DMSO-d6) δ 13.8, 22.0, 23.7, 27.3,
28.4, 28.5, 31.1, 51.7, 53.3, 75.1, 109.2, 115.1, 148.8, 154.2,
157.9, 162.0. Anal. Calcd for C16H24N4O3: C, 60.0; H, 7.6; N,
17.5. Found: C, 60.0; H, 7.8; N, 17.7.
4-Am in o-8-h ep t yl-5-m et h oxy-7-[(m et h oxyca r b on yl)-
a m in o)]p yr id o[4,3-d ]p yr im id in -2(1H)-on e (12). A solution
of 11 (0.160 g, 0.50 mmol) in a mixture of toluene (5.0 mL),
dichloromethane (2.0 mL), and triethylamine (1.0 mL) was
added dropwise to a 20% solution of phosgene in toluene (2.5
mL, 5.0 mmol). The mixture was stirred for 3 h, and then
ammonia gas was bubbled through for 30 min. The resulting
suspension was left stirring under an ammonia atmosphere
for 16 h. Water (15 mL) and ethyl acetate (15 mL) were then
added, and the aqueous layer was separated and extracted
with ethyl acetate (×4). The combined extracts were washed
with brine (50 mL) and dried (MgSO4), and the solvent was
evaporated. The dry residue was dissolved in 0.2 M sodium
methoxide in MeOH (5 mL), and the solution was stirred for
4 h. The solvent was evaporated, and the solid was partitioned
between saturated aqueous NaHCO3 (25 mL) and chloroform
(15 mL). The aqueous layer was separated and extracted with
chloroform (×4), the combined extracts were dried (MgSO4),
and the solvent was evaporated. Purification was achieved by
preabsorption (MeOH) onto silica gel followed by chromatog-
raphy twice (25 f 50% ethyl acetate/CH2Cl2, then 0 f 20%
methanol in dichloromethane) to give 12 (0.085 g, 47%) as a
H, m), 3.98 (1 H, t, J 7.4), 6.42 (1 H, br s), 6.81 (1 H, br s); 13
C
NMR (100 MHz; CDCl3) δ 14.0, 22.5, 26.8, 28.5, 28.7, 31.5,
32.9, 35.8, 54.6, 112.7, 113.1, 116.0, 167.8. Anal. Calcd for
C
13H18N4: C, 67.8; H, 7.9; N, 24.3. Found: C, 67.7; H, 8.1; N,
24.2.
4,6-Dia m in o-2-br om o-3-cya n o-5-h ep tylp yr id in e (8). Hy-
drogen bromide was bubbled into a solution of 7 (0.128 g, 0.56
mmol) in diethyl ether (45 mL) over a period of 2 h.6 Initially,
the mixture was kept at 0 °C but as the reaction proceeded it
was allowed to gradually warm to room temperature. Satu-
rated NaHCO3 (10 mL) was carefully added, followed by solid
sodium carbonate, until no further gas evolution was observed.
The aqueous layer was separated and extracted with ethyl
acetate (×3), the combined organic extract dried (Na2CO3), and
the solvent evaporated to give a yellow oil. Chromatography
(0 f 15% ethyl acetate in CH2Cl2) gave 8 (0.155 g, 90%) as a
white solid: mp 143-143.5 °C (from MeOH/H2O); 1H NMR
(400 MHz; CDCl3) δ 0.89 (3 H, t, J 6.9), 1.27-1.38 (8 H, m),
1.50 (2 H, quintet, J 7.8), 2.27 (2 H, t, J 7.8), 4.80 (2 H, s),
5.02 (2 H, s); 13C NMR (100 MHz; CDCl3) δ 14.0, 22.5, 24.7,
26.5, 29.1, 29.8, 31.7, 89.6, 99.4, 116.6, 140.8, 154.0, 157.9.
Anal. Calcd for C13H19BrN4: C, 50.2; H, 6.2; N, 18.0. Found:
C, 50.2; H, 6.2; N, 17.9.
3-Cya n o-4,6-d ia m in o-5-h ep tyl-2-m eth oxyp yr id in e (9)
a n d 5-Cya n o-4,6-d ia m in o-3-h ep t yl-2-m et h oxyp yr id in e
(10). Trinitrile 7 (0.474 g, 2.06 mmol) was added to a
methanolic solution of sodium methoxide prepared from
sodium (0.41 g, 18 mmol) and methanol (10 mL), and the
reaction was heated at reflux for 37 h.9 The solution was cooled
to room temperature and the solvent evaporated. Water (20
mL) was added and the mixture extracted with dichloro-
methane (×3). The combined organic extract was dried (Mg-
1
white solid: mp 165 °C dec; H NMR (400 MHz; DMSO-d6) δ
0.85 (3 H, t, J 6.8), 1.15-1.35 (10 H, br m), 2.64 (2 H, m), 3.65
(3 H, s), 3.94 (3 H, s), 7.64 (1 H, br s), 8.02 (1 H, br s), 9.44 (1
H, br s), 10.25 (1 H, br s); 13C NMR (100 MHz; DMSO-d6) δ
13.8, 22.0, 22.9, 28.2, 28.3, 28.5, 31.2, 51.7, 53.9, 90.6, 109.2,
148.6, 151.0, 154.2, 155.8, 157.7, 162.5; HRMS (FAB) found
m/z 364.2002 (M + H), C17H26N5O4 requires 364.1985.
4,7-Dia m in o-8-h ep tyl-1H,6H-p yr id o[4,3-d ]p yr im id in e-
2,5-d ion e (1). Chlorotrimethylsilane (0.30 mL, 0.26 g, 2.4
mmol) was added to a stirred suspension of 12 (0.146 g, 0.40
mmol) and sodium iodide (0.60 g, 4.0 mmol) in acetonitrile (30
mL), and the mixture was heated at reflux for 42 h with light
excluded. The reaction was cooled to 0 °C, and a solution of
NaHCO3 (0.5 g) and sodium thiosulfate pentahydrate (1.0 g)
(11) J unek, H.; Uray, G.; Kotzent, A.; Kastner, G. Monatsh. Chem.
1985, 116, 1199.

8484 J . Org. Chem., Vol. 64, No. 23, 1999
Mascal et al.
in water (25 mL) was added. The mixture was allowed to warm
to room temperature with stirring, and the precipitated
product was filtered and dried under vacuum to give 1 (0.085
g, 73%) as a pale yellow solid: mp 160 °C dec (from 4:1 DMF/
of the crystals to cryogenic temperatures dramatically reduced
the resolution of the diffraction pattern and introduced severe
mosaicity coupled with powder rings of “crystallized” solvent.
A complete dataset collected using synchrotron radiation and
a 30 cm MAR imaging plate permitted structure solution by
direct methods as described.1 Several attempts to model
partially occupied DMSO molecules in the remaining electron
density were carried out. In the final structure, the remaining
peaks were modeled as two partially occupied, restrained
DMSO molecules. This resulted in final conventional R values
of 0.1462 for 4134 Fo > 4σ(Fo) and 0.1643 for all 5725 data
1
DMSO); H NMR (400 MHz; DMSO-d6) δ 0.85 (3 H, t, J 6.6),
1.24 (10 H, br m), 2.37 (2 H, br m), 6.75 (2 H, br s), 7.46 (1 H,
br s), 8.84 (1 H, br s), 9.57 (1 H, br s), 11.37 (1 H, br s); 13C
NMR (100 MHz; DMSO-d6) δ 13.8, 21.3, 21.9, 28.2, 28.8, 31.3,
85.2, 86.0, 151.6, 152.8, 156.7, 162.1, 165.0; HRMS (FAB)
found m/z 292.1778 (M + H), C14H22N5O2 requires 292.1774.
Cr ysta lliza tion of 1. All manipulations were performed
under a nitrogen atmosphere. Crude 1 (ca. 6-8 mg) was placed
in a glass tube, and dry DMF or DMSO (ca. 2 mL) was added.
The mixture was warmed carefully until it became homoge-
neous and then filtered through glass wool into a second tube.
The filtrate was again warmed until it became homogeneous
before being allowed to cool undisturbed to room temperature.
After several hours, a crop of translucent crystals of cubic
morphology was observed. Freshly grown crystals mounted in
glass capillaries yielded good quality diffraction patterns with
a rotating anode source, although the quality deteriorated
markedly in the course of a few days. Attempts at rapid cooling
and a difference map with no feature above 0.29 e Å-3
.
Ack n ow led gm en t. This work was finacially sup-
ported by the EPSRC and BBSRC. Dr. A. J . Blake is
thanked for helpful advice on several occasions.
Su p p or t in g In for m a t ion Ava ila b le: 1H NMR and 13C
NMR spectra for compounds 1, 5, and 12. This material is
available free of charge via the Internet at http://pubs.acs.org.
J O990719T