The high-anti conformation of 7-halogenated 8-aza-7-deaza-2'- deoxyguanosines: A study of the influence of modified bases on the sugar structure of nucleosides

Article abstract of DOI:10.1002/(SICI)1522-2675(19990113)82:1<105::AID-HLCA105>3.0.CO;2-3

The conformation of the 7-bromo- and 7-iodo-substituted 8-aza-7- deazapurine nucleosides 1 and 2 in the solid state and in aqueous solution was studied by single-crystal X-ray analyses and by ¹H-NMR spectroscopy. In the solid state, both compou

Full text of DOI:10.1002/(SICI)1522-2675(19990113)82:1<105::AID-HLCA105>3.0.CO;2-3

Helvetica Chimica Acta ± Vol. 82 (1999)
105
The High-Anti Conformation of 7-Halogenated 8-Aza-7-deaza-2'-deoxy-
guanosines: A Study of the Influence of Modified Bases on the Sugar
Structure of Nucleosides
by Frank Seelaa)*, Georg Bechera), Helmut Rosemeyera), Hans Reuterb), Guido Kastnerb),
and Igor A. Mikhailopuloc)
a) Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück,
Barbarastr. 7, D-49069 Osnabrück, Germany
b) Anorganische Chemie, Institut für Chemie, Universität Osnabrück,
Barbarastr. 7, D-49069 Osnabrück, Germany
c) Institute of Bioorganic Chemistry, Byelorussian Academy of Sciences,
220141 Minsk, Zhodinskaya 5, Byelorussia
The conformation of the 7-bromo- and 7-iodo-substituted 8-aza-7-deazapurine nucleosides 1 and 2 in the
solid state and in aqueous solution was studied by single-crystal X-ray analyses and by 1H-NMR spectroscopy.
In the solid state, both compounds display a high-anti conformation around the glycosylic bond, and their 2'-
deoxy-b-d-ribofuranose moieties adopt an N-type sugar puckering. The orientation of the exocyclic C(4') C(5')
bond was found to be ap in both cases. In D2O solution, both compounds display i) an 8 ± 10% higher N-
conformer population than 2'-deoxyguanosine and ii) a preference of the sc conformation about the C(4') C(5')
bond. A comparative study on the influence of modified bases on the sugar structure of nucleosides is made.
Introduction. ± The conformational flexibility of nucleic acids can be more complex
than that of peptides because the sugar-phosphate backbone conformation is descibed
by five single-bond rotations in addition to five sugar torsions [1a]. It is expected that in
many cases, the conformational changes among nucleoside or nucleotide structures
obey a certain conformational pathway. This means that the movement of one torsion is
linearly coupled with another one [2] [3]. In general, the molecular structures of
nucleosides and nucleotides have been regarded as conformationally ꢀrigidꢁ [4]
probably due to the small variances of torsion angles. Besides gauche and anomeric
effects [5], important determinants of the overall structure of a nucleoside are the steric
and stereoelectronic effects of the nucleobases [6]. In a series of influential reports, at
first Gassen and coworkers [7], and later Chattopadhyaya and coworkers [8] have
demonstrated the importance of such effects on both the structure of a nucleoside as
well as on the secondary structure of a DNA molecule. Recently, our interest was
focussed on the stereoelectronic influence of modified nucleobases ± and here in
particular of aza- and deazapurines ± on the structure and stability of oligonucleotides
containing such compounds [9 ± 13]. We have observed that the incorporation of 8-aza-
7-deazapurine 2'-deoxynucleotides into oligodeoxynucleotides exerts an extraordinary
influence on their duplex stability which is significantly enhanced over that of the
parent unmodified oligomers [14 ± 16]. This may be traced to an altered secondary
structure of the base-modified oligomers with probably enhanced stacking interactions

106
Helvetica Chimica Acta ± Vol. 82 (1999)
and/or stronger H-bonds which might be similar to a ꢀverticalꢁ DNA with the
nucleobases being nearly parallel to the helix axis [1b] [17] [18].
In this communication, we report on the three-dimensional structures of two 7-
halogeno-substituted 8-aza-7-deaza-2'-deoxyguanosines 1 and 2, both in the solid state
and in aqueous solution. The unusual conformation of these nucleosides as well as
striking pecularities of their sugar-moiety structure prompted us to undertake a
detailed comparative study on more than 60 nucleosides with respect to the
interdependence of different structural parameters. The conformational control of
the biomolecular function of oligonucleotides by nucleoside building blocks such as 1
and 2 is discussed.
Results and Discussion. ± Syntheses. The synthesis of the nucleosides 1 and 2
recently described by us [19] was now improved by using different starting materials.
Thus, we undertook the preparation of the 7-bromo- and the 7-iodo-substituted 8-aza-
7-deaza-6-propoxypurines 5a,b (purine numbering is used throughout the General
Part) starting with compound 4 (obtained from 3; see Scheme 1). The halogenation
reaction was performed with either N-bromo- or N-iodosuccinimide (NXS, X ˆ Br
and I, resp.) in 1,2-dichloroethane and gave the desired compounds 5a,b in 64 ± 65%
yield [20].
Scheme 1
Subsequent glycosylation of 5a,b with 2-deoxy-3,5-di-O-(p-toluoyl)-a-d-erythro-
pentofuranosyl chloride (6) [21] resulted in the desired 7-halogenated nucleosides 7a,b
in 42 and 41% yield, respectively, together with the dehalogenated N8-nucleoside 8
(Scheme 2).

Helvetica Chimica Acta ± Vol. 82 (1999)
107
Scheme 2

108
Helvetica Chimica Acta ± Vol. 82 (1999)
Such a dehalogenation reaction has already been observed during the preparation
of corresponding alkoxy compounds [22]. Deblocking of 7a,b with 0.1m NaOPr/PrOH
furnished the unprotected nucleosides 9a,b. Hydrolysis of the propoxy groups of 9a,b
was performed in 1n NaOH (ca. 30 min at 608) yielding compounds 1 and 2. All new
compounds were characterized by 1H- and 13C-NMR spectroscopy (Table 1 and Exper.
Part) as well as by elemental analyses.
Table 1. 13C-NMR Chemical Shifts of 8-Aza-7-deazapurine Nucleobases and Related 2'-Deoxy-ribofuranosidesa)
C(7)b) C(5)b)
C(6)b)c) C(2)b)c) C(4)b)c)
C(1') C(2') C(3') C(4') C(5') OCH2
C(3)d) C(3a)d) C(4)d)c) C(6)d)c) C(7a)d)c)
1
2
4
122.0
101.9
131.7
98.4
93.7
95.6
95.4
89.2
96.2
91.7
98.1
96.0
90.1
158.1
157.5
163.5
163.0
162.9
163.0
163.1
164.9
162.9
163.0
156.3
155.1
162.1
162.5
161.9
162.6
162.2
163.5
162.4
162.0
156.5
155.8
158.9
159.4
159.0
158.7
159.3
162.3
158.5
158.1
83.1
83.2
±
±
±
83.4
83.4
90.1
83.2
83.2
37.6
37.7
±
±
±
34.8
34.8
36.8
37.5
37.4
70.8
70.9
±
±
±
74.9
75.0
74.9
70.1
70.9
87.4
87.4
±
±
±
81.3
81.3
82.0
87.4
87.4
62.4
62.4
±
±
±
64.0
64.1
64.3
62.3
62.4
±
±
67.3
67.4
67.1
67.6
67.5
67.4
67.5
67.4
5a 118.3
99.2
7a 119.9
b
b
100.2
124.8
8
9a 119.2
100.1
b
a) Measured in (D6)DMSO at 303K. b) Purine numbering. c) Tentative. d) Systematic numbering.
Conformation in the Solid State. The glycosylation site of the 8-aza-7-deazapurine
ring system (N(9)) and the b-d-anomeric configuration of nucleosides 1 and 2 were
confirmed by single-crystal X-ray analysis (Figs. 1 and 2).
Fig. 1. Molecular structure of 8-aza-7-bromo-7-deaza-2'-deoxyguanosine (1) in the solid state and atomic
numbering. Anisotropic displacement ellipsoids representing the 50% probability density of the corresponding
atoms are shown; H-atoms are shown as spheres with arbitrary radius.

Helvetica Chimica Acta ± Vol. 82 (1999)
109
Fig. 2. Molecular structure of 8-aza-7-deaza-2'-deoxy-7-iodoguanosine (2). For details in the solid state and
atom numbering, see legend to Fig. 1.
Both compounds show the high-anti conformation (space group P212121 (No. 19))
(Fig. 3) with very similar glycosylic torsion angles c(O(4') C(1') N(9) C(4): 92.9
and 93.2, resp.) [1c]. The sugar moieties of 1 and 2 exhibit both an N-type puckered
pentofuranose ring [1d] (Fig. 4) and the ap (g ) conformation about the C(4') C(5')
bond [1e]. This means that ± compared, e.g., to 2'-deoxyadenosine [9] ± in both cases,
the nucleobase and the CH2OH group undergo a disrotatory motion so that the
Coulomb repulsion between N(8) and O(5') as well as O(4') is minimized.
The crystal parameters are summarized in the Exper. Part. Bond lengths for both
compounds are listed in Table 2, bond angles in Table 3, and torsion angles in Table 4.
The nucleobases of both compounds 1 and 2 are planar, with their C- and N-atoms
showing a deviation of max. Æ0.052/0.043 Š1)2) from the least-squares plane of the
ring system. The bromo and iodo substituents show greater deviations from this plane.
The NH2 group atom N(2) lies 0.005(8)/0.013(7) Š1), the bromo/iodo substituents
X(7) 0.067(7)/0.094(6) Š1), and C(1') of the sugar unit 0.215(7)/0.182(6) Š1) below
the plane and the oxo group O(6) 0.033(8)/0.066(7) Š1) above this plane.
Both crystal structures are stabilized by the same H-bonding pattern (Fig. 5).
Because the iodo substitutent is larger than the bromo substituent, there are some
differences in the construction of the H-bond system and the van der Waals contacts.
Two strong H-bonds are observed in the solid state. The first of those strong bonds is
between H(3'O) and O(6) of a neighboring molecule bond A: d(H ´´´ O) ˆ 1.916(6)/
1.929(4) Š1), angle (O H ´´´ O) ˆ 160.6(2)8/165.8(2)81). The second strong H-bond
1
)
)
Values given first refer to compound 1, values given second refer to 2.
2
N(1) ˆ 0.047(4)/0.041(3) Š, C(2) ˆ 0.027(5)/ 0.014(4) Š, N(3) ˆ 0.025(4)/0.010(4) Š, C(4) ˆ
0.030(5)/0.023(4) Š, C(5) ˆ 0.052(5)/0.043(5) Š, C(6) ˆ 0.024(4)/0.020(4) Š, C(7) ˆ 0.008(5)/
0.008(4) Š, N(8) ˆ 0.049(4)/ 0.042(3) Š, N(9) ˆ 0.002(4)/0.009(3) Š.

110
Helvetica Chimica Acta ± Vol. 82 (1999)
Fig. 3. Perspective view of a) 8-aza-7-bromo-7-deaza-2'-deoxyguanosine (1) and b) 8-aza-7-deaza-2'-deoxy-7-
iodoguanosine (2) displaying the high-anti orientation of the base
links the H-atoms of the NH2 function, H(22), to Br(7)/I(7) in another neighboring
molecule bond B: d(H ´´´ X) ˆ 3.029(6)/3.045(4) Š1), angle (N H ´´´ X) ˆ 133.8(1)8/
141.9(1)81). In addition to these strong bonds, a number of weaker contacts exist which
are shown in Fig. 5. The main differences between 1 and 2 are summarized in Table 5.
To the best of our knowledge, these crystallographic analyses are the first which
describe the solid state structure of a b-d-2'-deoxyribonucleoside bearing an 8-aza-7-
deazapurine base. However, X-ray data of several corresponding b-d-ribonucleosides
as well as of other ꢀortho-azapurineꢁ or ꢀortho-azapyrimidineꢁ b-d-ribonucleosides (e.g.,
formycin or 6-azauridine) appeared in the literature [23 ± 25]. Like compounds 1 and 2,

Helvetica Chimica Acta ± Vol. 82 (1999)
111
Fig. 4. Perspective view of the 2'-deoxyribose conformation of a) 8-aza-8-bromo-7-deaza-2'-deoxyguanosine (1)
and b) 8-aza-7-deaza-2'-deoxy-7-iodo-guanosine (2)
all these nucleosides exhibit the unusual high-anti ( sc) conformation about the
glycosylic bond with a torsion angle c of ca. 908 which was assumed to be responsible
for their anomalous biophysical and biochemical behavior, both, on the monomeric as
well as on the polymeric level [26 ± 28].
Comparative Study on the Influence of Modified Bases on the Sugar Structure of
Nucleosides on the Basis of X-Ray Data. Inspection of the crystallographic data of
compounds 1 and 2 revealed some striking pecularities which prompted us to make a
comparative conformational study on a series of purine and pyrimidine b-d-ribo- and
2'-deoxy-b-d-ribonucleosides. This study uses X-ray data published earlier [29] and
correlates bond length differences with the torsion angle c around the glycosylic bond.
Steric and stereoelectronic effects of modified nucleobases exert a strong influence
on the conformation of the ribose moiety [30] as well as on the different bond lengths

112
Helvetica Chimica Acta ± Vol. 82 (1999)
Table 2. Bond Lengths [Š] for 1 (C10H12BrN5O4) and 2 (C10H12IN5O4)
Bond
1
2
Bond
1
2
N(1) C(2)
N(1) C(6)
C(2) N(3)
C(2) N(2)
N(3) C(4)
C(4) N(9)
C(4) C(5)
C(5) C(7)
C(5) C(6)
C(6) O(6)
C(7) N(8)
1.373(9)
1.414(9)
1.326(8)
1.315(9)
1.344(7)
1.356(7)
1.400(8)
1.404(8)
1.428(9)
1.215(8)
1.309(8)
1.367(6)
1.383(6)
1.321(6)
1.334(6)
1.349(6)
1.358(5)
1.386(6)
1.425(6)
1.431(6)
1.225(6)
1.316(6)
C(7) Br7
C(7) I(7)
1.876(5)
2.060(4)
1.387(5)
1.441(5)
1.428(6)
1.517(6)
1.504(6)
1.421(5)
1.507(6)
1.436(5)
1.426(7)
N(8) N(9)
N(9) C(1')
C(1') O(4')
C(1') C(2')
C(2') C(3')
C(3') O(3')
C(3') C(4')
C(4') O(4')
C(5') O(5')
1.393(6)
1.443(7)
1.432(6)
1.529(7)
1.516(7)
1.426(6)
1.519(7)
1.442(6)
1.400(8)
Table 3. Bond Angles [8] for 1 (C10H12BrN5O4) and 2 (C10H12IN5O4)
Angle
1
2
Angle
1
2
N(3) C(2) N(1)
N(2) C(2) N(1)
C(2) N(3) C(4)
N(3) C(4) N(9)
N(3) C(4) C(5)
N(9) C(4) C(5)
C(4) C(5) C(7)
C(4) C(5) C(6)
C(7) C(5) C(6)
N(1) C(6) C(5)
N(8) C(7) C(5)
N(8) C(7) Br(7)
C(5) C(7) Br(7)
C(5) C(7) I(7)
C(7) N(8) N(9)
123.5(6)
116.8(6)
112.6(5)
125.7(5)
128.5(4)
105.8(5)
104.4(5)
118.8(5)
136.6(5)
110.7(5)
113.8(5)
119.9(4)
126.2(5)
±
123.4(4)
116.6(4)
112.4(4)
124.8(4)
128.3(3)
106.9(4)
104.8(3)
118.5(4)
136.6(4)
111.0(4)
111.7(4)
±
C(4) N(9) N(8)
C(4) N(9) C(1')
N(8) N(9) C(1')
O(4') C(1') N(9)
O(4') C(1') C(2')
N(9) C(1') C(2')
C(3') C(2') C(1')
O(3') C(3') C(2')
O(3') C(3') C(4')
C(2') C(3') C(4')
O(4') C(4') C(5')
O(4') C(4') C(3')
C(5') C(4') C(3')
C(1') O(4') C(4')
112.6(5)
126.5(5)
119.9(4)
108.4(4)
106.6(4)
113.0(5)
104.8(4)
109.1(4)
114.2(4)
102.9(4)
107.6(4)
104.6(4)
114.6(4)
109.7(4)
111.5(3)
127.7(4)
119.9(3)
109.1(4)
106.5(3)
112.9(4)
105.1(3)
108.9(3)
114.6(3)
103.4(3)
107.9(4)
105.4(3)
115.0(4)
110.2(3)
±
126.9(3)
105.1(3)
103.4(4)
Table 4. Torsion Angles for the Sugar Units of 1 (C10H12BrN5O4) and 2 (C10H12IN5O4)
Torsion angle
1
2
Torsion angle
1
2
C(4) N(9) C(1') O(4')
N(8) N(9)) C(1') O(4')
C(4) N(9) C(1') C(2')
N(8) N(9) C(1') C(2')
O(4') C(1') C(2') C(3')
N(9) C(1') C(2') C(3')
C(1') C(2') C(3') O(3')
C(1') C(2') C(3') C(4')
N(9) C(1') O(4') C(4')
93.2(6)
74.3(6)
148.8(5)
43.7(7)
11.0(7)
108.0(5)
148.8(5)
27.1(6)
132.8(5)
92.9(5) C(2') C(1') O(4') C(4')
75.0(5) C(1') O(4') C(4') C(5')
148.9(4) C(1') O(4') C(4') C(3')
43.2(6) O(3') C(3') C(4') O(4')
13.9(5) C(2') C(3') C(4') O(4')
105.9(4) O(3') C(3') C(4') C(5')
149.2(4) C(2') C(3') C(4') C(5')
26.9(5) O(4') C(4') C(5') O(5')
127.9(4) C(3') C(4') C(5') O(5')
10.8(6)
150.6(5)
28.3(6)
151.9(5)
33.9(6)
90.4(6)
151.5(5)
53.3(8)
169.2(6)
5.7(4)
146.4(4)
23.0(4)
149.2(4)
30.6(4)
92.2(5)
149.3(4)
54.1(6)
171.5(5)
such as N(9 or 1) C(1'), C(1') O(4'), and O(4') C(4') [31]. The N-glycosylic bond is
usually significantly longer than the adjacent C(1') O(4') bond. Recently, a linear
dependence of the torsion angle c from the bond-length difference of the bonds
C(4') O(4') and O(4') C(1') was reported which was looked upon as a manifestation
of the anomeric effect [32] [33]. An extended version of the graph [C(4') O(4')] ±
[O(4') C(1')] vs. c is now given in Fig. 6. It is based on the X-ray data of 64 purine and

Helvetica Chimica Acta ± Vol. 82 (1999)
113
Fig. 5. Hydrogen bonding system of compounds 1 and 2 in the solid state
Table 5. Hydrogen Bond Lengths d(H ´´´ X) [Š] in the Solid State of 1 (C10H12BrN5O4) and 2 (C10H12IN5O4)
Bond
1
2
Bond
1
2
A
B
C
D
1.916(6)
3.029(6)
3.358(6)
2.535(8)
1.929(4)
3.045(4)
3.447(5)
2.423(6)
E
2.522(7)
2.314(6)
2.439(6)
2.764(5)
2.379(5)
2.337(5)
F
pyrimidine ribo- and 2'-deoxyribonucleosides [29] including compounds 1 and 2
described above (see Table 6).
Fig. 7 shows the dependence of c from the bond-length difference of the bonds (N(9
or 1) C(1') and C(1') O(4') taken from the X-ray analyses (Table 6). Also here, a
linear correlation can be observed. Obviously, the difference in bond length between
C(4') O(4') and O(4') C(1') (0 ± 7 pm) and N(9 or 1) C(1') and C(1') O(4') (0 ±
12 pm) regulates the sugar puckering and therewith the torsion angle about the N-
glycosylic bond (c). From the graphs it can be seen that compounds 1 and 2 as well as
other ꢀortho-azapurineꢁ and ꢀortho-azapyrimidineꢁ nucleosides, adopting the high-anti
conformation, exhibit almost equal bond-length values.
The bond-length differences discussed above are obviously influenced by the p-
electron system of the base. Unusually high or low c values which deviate strongly
from the graph are the result of intramolecular H-bonds or steric interactions
(repulsion or attraction). Examples are guanosine, 2'-deoxyguanosine, or 1-deazagua-
‡
nosine [34] [35]. Here, a H-bond between the 5'-OH group in the ‡ sc (g )
conformation and either N(3) (1-deazapurines) or the 2-NH2 group of guanine causes
the relatively unusual syn conformation of the base (Figs. 6 and 7).
It is well-established that the p-electron density in the heterocyclic systems of the
bases is conducted through the adjacent furanose atoms C(1'), O(4') and C(4'),
explaining ± in part ± the shortening of the C(1') O(4') bond relative to C(4') O(4').
This is due to a s-resonance of the lone electron pairs at O(4') with the electronic
system of the heterocycle by through-bond and through-space interactions [30]. Apart

114
Helvetica Chimica Acta ± Vol. 82 (1999)
Fig. 6. Bond-length difference of the bonds C(4') O(4') and O(4') C(1') vs. the torsion angle
c
(O(4') C(1') N(9 or 1) C(4 or 2)) of 64 ribo- and 2'-deoxyribonucleosides according to the Entries 1 ± 64
of Table 6 (see [29])
Fig. 7. Bond-length difference of the bonds N(9 or 1) C(1') and C(1') O(4') vs. c of 64 ribo- and 2'-deoxyribo-
nucleosides according to the Entries 1 ± 64 of Table 6 (see [29])

Helvetica Chimica Acta ± Vol. 82 (1999)
115
Table 6. Torsion Angle c and Bond-Length Differences of Purine and Pyrimidine Nucleosidesa).
Entry c [8] Bond
Bond
Bond
Entry c [8] Bond
Bond
Bond
(see
N(9 or 1) C(1') C(1') O(4') C(4') O(4') (see
N(9 or 1) C(1') C(1') O(4') C(4') O(4')
[29])
[pm]
[pm]
[pm]
[29])
[pm]
[pm]
[pm]
1
2
3
4
5
6
7
8
9
45.0 143.6
107.0 143.8
114.6 144.4
122.2 144.5
133.4 145.2
127.2 145.2
122.9 145.4
114.5 145.9
130.9 146.0
127.7 146.7
137.9 146.7
83.4 146.6
36.3 146.8
76.0 146.6
136.9 146.0
170.1 146.7
146.0 147.0
128.6 147.4
153.3 147.5
138.2 147.6
140.9 148.0
160.4 149.2
159.7 149.4
161.9 149.6
161.7 149.7
154.4 150.4
162.0 149.0
150.6 148.1
154.6 149.0
137.9 146.7
129.0 146.4
119.0 142.7
140.9
142.2
142.0
141.5
141.2
142.6
141.3
142.0
141.6
140.2
141.6
141.3
141.0
141.6
141.5
141.1
140.3
141.0
140.7
142.0
143.4
142.3
140.5
141.0
141.2
139.0
141.3
141.0
139.5
141.6
142.2
143.2
145.6
145.1
146.1
144.1
145.5
143.5
141.7
145.0
145.2
144.6
146.0
143.4
144.5
145.5
145.4
145.0
146.3
144.8
144.4
144.7
146.0
146.3
144.9
145.8
144.5
146.1
145.4
146.0
146.3
146.0
146.5
146.0
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
58.9 147.3
176.0 149.2
53.3 150.2
58.8 145.8
52.6 145.8
70.5 144.6
58.1 145.3
139.6 147.8
112.8 145.1
158.1 152.4
156.7 146.7
162.9 148.8
162.8 149.7
172.5 150.8
137.7 147.1
158.8 148.9
131.7 146.1
164.2 149.4
174.7 150.9
129.1 147.1
93.2 144.3
92.9 144.0
70.0 147.1
104.0 144.9
147.0 145.3
111.0 146.6
119.0 147.5
115.0 144.8
93.3 146.2
109.8 150.2
90.7 144.1
56.1 145.3
141.7
143.6
140.8
141.0
140.4
146.8
141.2
141.7
143.3
140.8
144.5
141.1
141.2
140.4
143.2
142.0
142.4
141.1
141.0
144.0
143.2
142.8
142.1
143.3
141.6
141.6
141.6
143.4
143.3
143.9
142.7
141.4
146.1
149.3
144.1
145.8
145.4
145.7
145.6
145.0
144.2
145.8
147.9
144.8
144.5
146.0
145.5
146.0
144.5
144.4
146.5
145.1
144.2
143.6
145.1
144.2
146.8
143.5
143.9
144.4
143.9
145.4
143.7
146.0
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
a) For compound names (Entries 1 ± 64) and references for crystallographic data; see [29].
from these stereoelectronic effects, another factor has to be taken into account: the
O(4') atom carries a net charge of 0.16 e, suggesting that it is a weak H-bridge
acceptor, and, in fact, H-bonds to this atom have been observed in a few nucleoside
crystal structures. Especially in the case of favorable configurational juxtaposition of
O(4') and OH groups, such H-bonds appear feasible [1f,g].
As the p-electron excess of the imidazole moiety of a purine is strongly reduced by
the p-deficient pyrimidine system, the C(8) atom becomes the most electron-deficient
site in the non-ionized molecule, and, thus, H C(8) is the most acidic proton bound to
a purine-ring C-atom [36]. This is promoted by electron-withdrawing substituents. The
same is true for H C(6) of a pyrimidine ring. As a consequence, one can assume an
attractive interaction between H C(8) of a purine or H C(6) of a pyrimidine and
O(4') of an attached sugar ring, especially when c ranges around 1808 [37a]. Such an

116
Helvetica Chimica Acta ± Vol. 82 (1999)
attractive interaction should lead to a deformation of the furanose ring with bond
stretching and bond shortening as depicted in Fig. 8.
Fig. 8. Bond stretching ( !) and shortening (! ) within the sugar moiety of a nucleoside due to
stereoelectronic effects and hydrogen bonding. Stretchings and shortenings are exaggerated for a better
visualization.
Both effects, the stereoelectronic effect of the heterocycle via through-bond as well
as through-space interactions and an attractive interaction between an acidified
H
C(8) or H C(6), respectively, and O(4'), would act in the same direction, namely a
highly negative c value (anti conformation) as well as the particular bond-length
alterations which are indeed observed. On the other hand, the reduced acidity of
H
C(8) (purines) or H C(6) (pyrimidines) or the introduction of an N-atom into
position 8 of a purine or position 6 of a pyrimidine moiety leads to a distorsion of c
towards the high-anti range. This induces a change of the sugar puckering from S to N as
in the latter conformation, the steric repulsion between Hb C(2') and N(8) (or N(6)) is
minimized. Indeed N-type puckering has been found for ꢀortho-azanucleosidesꢁ in the
crystal and also in the case of the 8-aza-7-deaza-2'-deoxyguanosines 1 and 2.
Conformation of Compounds 1 and 2 in Solution. As in the solid state, nucleosides
exist in various conformations in solution. The topology of a nucleoside in solution is
decided mainly by two dynamic two-state and one three-state equilibria: i) the syn-anti
equilibrium of the base about the glycosylic bond, ii) the sugar puckering (N>S,
‡
3'
T >3'T2'), and iii) the rotational equilibrium about the C(4') C(5') bond (gg >gt>
2'
gg ). These equilibria are interdependent, and the energy barrier between the most
preferred conformational states is usually low [1d].
The conformational analysis of the furanose puckering of compounds 1 and 2 was
performed by the PSEUROT program (version 6.2) [37b] which calculates best fits
of experimental 3J(H, H) values (3J(1',2'), 3J(1',2''), 3J(2',3'), 3J(2'',3'), and 3J(3',4')) to
the five conformational parameters (P and ym for both N- and S-type conformers and
corresponding mole fractions). The populations of the staggered rotamers across the
C(4') C(5') bond were calculated from 3J(4',5') and 3J(4',5'') according to Westhof et al.
[38]. The data are presented in Table 7.
For comparison, the data of 2'-deoxyguanosine (Gd) [10], 7-deaza-2'-deoxyguano-
sine (c7Gd) [10], 8-aza-7-deaza-2'-deoxyguanosine (c7z8Gd) [10], as well as of 8-aza-7-
cyano-7-deaza-2'-deoxyguanosine (CN7c7z8Gd) are included [39]. Scrutiny of the
conformational data reveals that the 8-aza-7-deazapurine 2'-deoxynucleosides exhibit

Helvetica Chimica Acta ± Vol. 82 (1999)
117
all a significantly more pronounced N-conformer population compared to Gd as well as
to c7Gd. Within the series of 8-aza-7-deaza-2'-deoxynucleosides, the 7-cyano derivative
shows the highest N-conformer population (46%), while the 7-halogeno derivatives 1
and 2 exhibit almost the same values as the unsubstituted parent compound c7z8Gd.
These findings are due to the stereoelectronic effect of the 7-cyano substituent and are
in line with results observed for corresponding 7-deazapurine nucleosides. Interest-
ingly, the 7-halogeno derivatives of c7z8Gd crystallize in the pure N-form as the sole
crystalline state. This has already been observed for 7-deaza-2'-deoxyadenosine and its
7-nitro derivative [40].
Table 7. 3J(H,H) Coupling Constants of the Sugar Moieties and Conformer Populations of 2'-Deoxynucleosides
at 303 Ka)
3J(H,H) [Hz]b)
1',2' 1',2'' 2',3' 2'',3' 3',4' 4',5' 4',5'' %N %S %gg %gt %gg PN PS
Conformation
Pseudorotational Parameters
ym(N) ym(S)
‡
1
2
6.55 6.65 6.20 3.85 4.30 4.60 6.00 39 61 27
6.55 6.65 6.50 4.10 3.70 4.30 6.00 37 63 30
44 29
44 25
47 28
43 26
33 24
30 17
19 152.1 36
31.5
30.3
35.6
30.4
30.1
32.1
19 160.7 36
19 159.9 36
19 157.8 36
19 157.2 36
19 160.5 36
CN7c7z8Gd 6.10 6.45 6.00 4.65 4.40 4.60 6.20 46 54 25
c7z8Gd
c7Gd
Gd
6.65 6.65 6.25 3.65 3.90 4.30 5.90 36 64 31
7.25 6.50 6.25 3.00 3.35 4.20 5.00 28 72 43
7.30 6.50 6.30 3.60 3.20 3.60 4.70 29 71 53
a) Solvent, D2O; r.m.s. ꢀ 0.4 Hz; j DJmax jꢀ 0.4 Hz. b) Primed and doubly primed locants are used to distinguish
between the two protons at C(2') or C(5').
Concerning the conformation about the C(4') C(5') bond, also an interesting
relationship can be seen from Table 7. While Gd exhibits a ‡ sc rotamer population of
‡
53% (gg ), it is diminished to 31% in the case of c7z8Gd, while the populations of the
other two staggered conformers are enhanced by an almost equal amount. Introduction
of 7-substituents decreases the ‡ sc population further, whereby the compound with
the most electron-withdrawing substituent (CN) exhibits the lowest value (CN7c7z8Gd,
‡
25% gg ). This trend is opposite to that found for 7-substituted 7-deazapurine
nucleosides [9].
Temperature-Dependent CD and UV Measurements on Oligonucleotides Containing
Compounds 1 or 2. To shed more light on the conformational control of the structure
and stability of oligodeoxynucleotides by the conformation of compounds 1 or 2,
temperature-dependent CD spectra of Br7c7z8Gd (1), I7c7z8Gd (2), and the parent c7z8Gd
as well as of the homooligomer 5'-(I7c7z8Gd)6 were measured (10 mm Na-cacodylate
buffer, 10 mm MgCl2, 100 mm NaCl (pH 7.0); 10 ± 908) (Fig. 9). As can be seen from
Fig. 9,b, the homooligomer exhibits an unusual CD spectrum at room temperature, the
Cotton effects of which are changed at high temperature: at 908 the CD spectrum
displays a similar shape as those reported for homooligonucleotides built-up from (8-
2')-bridged nucleotides [41] [42] in which the high-anti conformation of the bases is
chemically locked.
The temperature dependence of the CD spectrum of the homooligomer implies
strong stacking interactions between the bases. This could be verified by measuring the
temperature-dependent UV spectra of 5'-(I7c7z8Gd)6 as well as of 5'-(Br7c7z8Gd)6 [43].
Fig. 10 displays cooperative melting curves of these homomers in a 1:1 mixture of

118
Helvetica Chimica Acta ± Vol. 82 (1999)
10 mm Na-cacodylate buffer (10 mm MgCl2, 100 mm NaCl, pH 7) and formamide from
which Tm values of ca. 528 and 548, respectively, could be estimated. In pure buffer, the
Tm values range above 858. This cooperative melting represents either single-strand
destacking or a dissociation of a duplex.
Relevance of a Conformational Preorganization of a Nucleoside Structure for the
Biomolecular Function of an Oligonucleotide. Evidence that the conformational
properties of base-modified nucleosides are maintained in short nucleic-acid fragments
exerting influence on the structure and stability of corresponding oligonucleotides was
first described between 1978 ± 1983 by Gassen and coworkers [7] who demonstrated the
influence of 5-substituted uridine derivatives on the conformation and base/base
stacking interactions within di-, tri-, and tetraribonucleotides of the (A-U) type. They
were able to prove that electron-attracting substituents such as NO2 or halogeno
enhance the base/base interaction while electron donating groups (NH2) diminish the
Fig. 9. CD Spectra of a) I7c7z8Gd, Br7c7z8Gd, and c7z8Gd at 108 and b) 5'-d(I7c7z8G)6 at 10 and 908. In 10 mm Na-
cacodylate, 10 mm MgCl2, 100 mm NaCl (pH 7).

Helvetica Chimica Acta ± Vol. 82 (1999)
119
Fig. 10. Melting curves of 5'-(I7c7z8Gd)6 and 5'-(Br7c7z8Gd)6. In 10 mm Na-cacodylate, 10 mm MgCl2, 100 mm
NaCl (pH 7)/formamide 1:1 (v/v).
stacking. Also Chattopadhyaya and coworkers demonstrated in a convincing manner
the decisive importance of intramolecular stereoelectronic effects within a nucleoside
on the secondary structure of an oligonucleotide [44]: they demonstrated by NMR
spectroscopy that the unmodified oligomer 5'-d(CGCGAATTCGCG) exists entirely in
a B-DNA form, whereas a corresponding analogue containing the carbocyclic
nucleoside 2'-deoxyaristeromycin instead of Ad, which does not show the stabilizing
stereoelectronic effect in the cyclopentane moiety, exists in a dynamic equilibrium as
hairpin and duplex (1:1, ct ˆ 2 mm).
The more pronounced N-type sugar pucker of compounds 1 and 2 should merge an
oligonucleotide towards an A-type secondary structure. If this is the case, hybridization
with a complementary oligoribonucleotide should be increased. However, this is not
the case due to the high-anti conformation of these base-modified nucleosides [45].
This unusual conformation might be the reason why 5'-triphosphates of 8-aza-7-
deazapurine 2'-deoxyribonucleosides are not as efficient substrates for various DNA
polymerases [46] as the corresponding triphosphates of 7-deazapurine b-d-2'-
deoxyribonucleosides.
Homooligonucleotides built-up exclusively from such 8-aza-7-deazapurine 2'-
deoxyribonucleoside building blocks should adopt a secondary structure which is
neither a B- nor an A-DNA but probably a vertical DNA with strongly stacked bases in
an almost parallel orientation to the helix axis. This assumption is cherished by results
reported by Olson and Dasika who predicted, on the basis of a theoretical analysis, the
preferred conformational parameters of such an unusual DNA structure [17] [18].
These are i) a high-anti conformation of the bases, ii) an N-type sugar pucker, and
iii) an ap conformation about the C(4') C(5') bond ± all conformations which have
been established for compounds 1 and 2. Such a secondary nucleic-acid structure has
been realized for polynucleotides built-up from modified purine nucleotides with a
covalent bridge between C(8) and C(2') locking the base in the high-anti conformation
[41] [42].

120
Helvetica Chimica Acta ± Vol. 82 (1999)
Nevertheless, oligodeoxyribonucleotides containing only a few 8-aza-7-deaza- or 8-
azapurine 2'-deoxynucleotides adapt to the general B-DNA structure forming
stabilized duplexes due to enhanced stacking interactions.
The authors gratefully acknowledge financial support by the Boehringer Mannheim GmbH, Germany. We
thank Dr. R. Marumoto, Tokyo, for collecting the X-ray data of 2'-deoxyguanosine available.
Experimental Part
1. General. Flash chromatography (FC): at 0.4 bar on silica gel 60 H (Merck, Darmstadt, Germany). Thin-
layer chromatography (TLC): Aluminium sheets silica gel 60 F254 (0.2 mm; Merck, Darmstadt, Germany). TLC
Scanning: CS-930-TLC scanner (Shimadzu, Japan). Solvent systems for FC and TLC: CH2Cl2/MeOH 98:2 (A),
CH2Cl2/MeOH 95:5 (B), CH2Cl2/MeOH 9:1 (C), CH2Cl2/acetone 98:2 (D), CH2Cl2/acetone 95:5 (E). M.p.:
Büchi-SMP-20 apparatus (Büchi, Switzerland); not corrected. UV Spectra: a 150-20 spectrometer (Hitachi,
Japan). NMR Spectra: AC-250 and AMX-500 spectrometer (Bruker, Germany); d values in ppm downfield from
internal SiMe4 (1H, 13C). Microanalyses were performed by Mikroanalytisches Labor Beller (Göttingen, Germany).
2. X-Ray Crystal Structure of 6-Amino-3-bromo-1-(2-deoxy-b-d-erythro-pentofuranosyl)-1,5-dihydro-4H-
pyrazole[3,4-d]pyrimidin-4-one (1) and 6-Amino-1-(2-deoxy-b-d-erythro-pentofuranosyl-1,5-dihydro-3-iodo-
3
4H-pyrazolo[3,4-d]pyrimidin-4-one (2). Crystal Data ). Single crystals (size 0.45 Â 0.15 Â 0.15 mn for 1 and
0.45 Â 0.15 Â 0.09 mn for 2) were prepared as described and fixed at the top of a Lindemann capillary with epoxy
resin.
C10H12BrN5O4 (1) and C10H12IN5O (2); both orthorhombic and space group P212121 (No. 19), a ˆ 20.429(3)/
20.371(2)1), b ˆ 7.275(1)/7.339(1)1), c ˆ 8.216(1)/8.4881(1) Š1), Vˆ 1221.0(2)/1269.0(3) Š3 1); Z ˆ 4/41), Dx ˆ
1.883/2.058 Mg m 3 1), m ˆ 3.391/2.547 mm 1 1), F(000) ˆ 696/7981), T 293(2) K for both.
Data Collection and Processing. Data for both compounds were collected on a Siemens-P4-four-cycle
diffractometer with MoKa radiation ( ) 0.71073 Š and a graphite monochromator [47]. A total of 2829/33291)
reflections were collected in a range of 2.488 ꢀ q ꢀ 25.008/2.0081) ꢀ q ꢀ 22.998, giving 2055/17201) independent
reflections (R(int) 0.0488/0.02081)). An absorption correction was carried out using y-scans (Tmin 0.4975/
0.66371), Tmax 0.9002/0.99741)).
Solution and Refinement. Both structures were solved by standard direct methods. Full-matrix least-squares
refinements based on F20 were performed with non-H-atoms assigned anisotropic thermal parameters. All H-
atoms were found in difference Fourier syntheses but were constructed in geometrically reasonable positions
(bond lengths, bond angles). Especially the planar geometry of the NH2 group and its orientation relative to the
ring atoms was confirmed from difference Fourier synthesis. For all H-atoms, a common isotropic thermal
parameter was refined.
Programs from the Siemens SHELXTL program package were used for the solution, refinement, and
graphical representation of the structures [47]. A total of 182/1841) parameters were refined, so that a data-to-
parameter ratio of 11.2/9.31) resulted. The final R1 and wR2 values for data with I > 2s(I) were 0.0435/0.02261)
and 0.903/0.05981). Corresponding values for all data were 0.0538/0.02351) and 0.0950/0.06101). The goodness-
of-fit based on F20 was 1.030/1.1091). The absolute structure parameter was refined to 0.03(2)/ 0.04(3). The
final difference Fourier map had peak maxima and minima at 0.457/0.2851) and 0.401/ 0.271 e Š 3 1), without
any configurational relevance.
3. Syntheses. 4-Propoxy-1H-pyrazolo[3,4-d]pyrimidin-6-amine (4). A soln. of 4-chloro-1H-pyrazolo[3,4-
d]pyrimidin-6-amine [48] (6.8 g, 0.04 mmol) in 1m NaOPr/PrOH (100 ml) was refluxed for 1 h. Upon cooling,
NaCl was precipitated with Et2O (100 ml) and was filtered off. The filtrate was neutralized with 96% AcOH and
evaporated. The residue was dissolved in MeOH and precipitated as pale-yellow needles by addition of ice-cold
H2O. Recrystallization from aq. MeOH yielded 4 (3.3 g, 70%) Colorless needles. M.p. 2118. TLC (silica gel, C):
Rf 0.6. UV (MeOH): 244(5100), 276(6600). 1H-NMR ((D6)DMSO): 0.92 (t, J ˆ 5.9, Me); 1.7 (m, CH2);
4.31 (t, J ˆ 6.4, CH2O); 6.52 (s, NH2); 7.75 (s, H C(3)); 12.8 (s, NH). Anal. calc. for C8H11N5O (193.2):
C 49.73, H 5.74, N 36.25; found: C 49.53, H 5.74, N 36.10.
3
)
Crystallographic data (excluding structure factors) have been deposited with the Cambridge Crystal-
lographic Data Centre as deposition No. CCDC-106122 and CCDC-106123 for 1 and 2, respectively.
Copies of the data can be obtained, free of change, on application to the CCDC, 12 Union Road,
Cambridge CB2 1EZ, UK (fax: ‡ 44(0)1223-336033 or e-mail: deposit@ccdc. com.oc.uk).

Helvetica Chimica Acta ± Vol. 82 (1999)
121
3-Bromo-4-propoxy-1H-pyrazolo[3,4-d]pyrimidin-6-amine (5a). To a soln. of 4 (1.0 g, 5.2 mmol) in 1,2-
dichloroethane (50 ml), N-bromosuccinimide (1.0 g, 5.6 mmol) was added. After heating under reflux for 1 h,
the solvent was evaporated to yield an orange solid which was washed with H2O (2 Â 100 ml), filtered off, and
dissolved in MeOH. Decolorization with charcoal, filtration, and addition of ice-cold water to the filtrate gave a
yellowish precipitate. Recrystallization from aq. MeOH yielded 5a (0.91 g, 64%) colorless needles. M.p. 2218
(dec.). TLC (silica gel, C): Rf 0.7. UV (MeOH): 248 (6100), 274 (7100). 1H-NMR ((D6)DMSO): 0.99 (t, J ˆ
5.6, Me); 1.74 (m, CH2); 4.33 (t, J ˆ 6.4, CH2O); 6.79 (s, NH2); 13.05 (s, NH). Anal. calc. for C8H10BrN5O
(272.1): C 35.31, H 3.7, N 25.74; found: C 35.47, H 3.77, N 25.67.
3-Iodo-4-propoxy-1H-pyrazolo[3,4-d]pyrimidin-6-amine (5b). As described for 5a, with 4 (1.0 g, 5.2 mmol)
and N-iodosuccinimide (1.3 g, 5.7 mmol, 2 h); 5b (1.1 g, 65%). Colorless needles M.p. 2238. TLC (silica gel, C):
Rf 0.7. UV (MeOH): 248 (6000), 274 (7000). 1H-NMR ((D6)DMSO): 1.07 (t, J ˆ 5.8, Me); 1.77 (m, CH2);
4.35 (t, J ˆ 6.4, CH2O); 6.7 (s, NH2); 13.08 (s, NH). Anal. calc. for C8H10IN5O (319.1): C 30.11, H 3.16, N 21.95;
found: C 30.26, H 3.17, N 21.89.
3-Bromo-1-[2-deoxy-3,5-di-O-(p-toluoyl)-b-d-erythro-pentofuranosyl]-4-propoxy-1H-pyrazolo[3,4-d]pyr-
imidine-6-amine (7a) and 2-[2-Deoxy-3,5-di-O-(p-toluoyl)-b-d-erythro-pentofuranosyl]-4-propoxy-1H-pyrazo-
lo[3,4-d]pyrimidine (8). A suspension of powdered KOH (1.24 g, 22 mmol) and 5a (5.5 mmol) in anh. MeCN
(100 ml) was stirred for 10 min at r.t. Then, TDA-1 (ˆ tris[2-(2-methoxyethoxy)ethyl]amine; 200 ml, 0.6 mmol)
was added, and stirring was continued for another 10 min. Then, 2-deoxy-3,5-di-O-(p-toluoyl)-a-d-erythro-
pentofuranosyl chloride (6) [3] (2.56 g, 6.6 mmol) was added in portions. After 20 min, insoluble material was
filtered off, and the filtrate was evaporated. The resulting foam was applied to FC (silica gel, column 15 Â 6 cm,
D, then E): 7a (from the faster-migrating zone) and 8 from the slower-migrating zone).
Data of 7a: 1.3 g, 42% of colorless foam. TLC (silica gel, D): Rf 0.43. UV (MeOH): 243 (38500),
276 (10900). 1H-NMR ((D6)DMSO): 1.02 (t, J ˆ 7.0, Me); 1.78 (m, CH2); 2.36, 2.40 (2s, 2 MeC6H4);
2.66 (m, Ha C(2')); 3.17 (m, Hb C(2')); 4.37 ± 4.46 (m, CH2O, 2 H C(5'), H C(4')); 5.73 (m, H C(3'));
6.55 (ꢀtꢁ, J ˆ 5.7, H C(1')); 7.07 (s, NH2); 7.28 ± 7.92 (4d, J ˆ 8.1, 2 MeC6H4). Anal. calc. for C29H30BrN5O6
(624.5): C 55.78, H 4.84, N 11.20, found: C 55.86, H 4.86, N 11.05.
Data of 8: 620 mg (17%) of colorless foam. TLC (silica gel, B): Rf 0.53. UV (MeOH): 240 (35100),
283 (9500), 296 (8700). 1H-NMR ((D6)DMSO): 0.94 (t, J ˆ 7.3, Me); 1.75 (m, CH2); 2.34, 2.38 (2s, 2 MeC6H4);
2.74 (m, Ha C(2')); 3.10 (m, Hb C(2')); 4.26 ± 4.57 (m, CH2O, 2 H C(5'), H C(4')); 5.82 (m, H C(3'));
6.40 (ꢀtꢁ, J ˆ 5.6, H C(1')); 6.46 (s, NH2); 7.24 ± 7.92 (4d, J ˆ 8.1, 2, MeC6H4); 8.45 (s, H C(3)). Anal. calc. for
C29H31N5O6 (545.6): C 63.84, H 5.73, N 12.84; found: C 63.73, H 5.70, N 12.84.
1-[2-Deoxy-3,5-di-O-(p-toluoyl)-b-d-erythro-pentofuranosyl]-3-iodo-4-propoxy-1H-pyrazolo[3,4-d]pyri-
midin-6-amine (7b) and 8. As described for 7a, with 5b (5.5 mmol): 7b (1.4 g, 41%). White foam of TLC (silica
gel, D): Rf 0.44. UV (MeOH): 243 (38000), 276 (10500).1H-NMR ((D6)DMSO): 1.02 (t, J ˆ 7.2, Me);
1.79 (m, CH2); 2.38, 2.40 (2s, 2MeC6H4), 2.66 ( m, Ha C(2')), 3.19 (m, Hb C(2')), 4.37 ± 4.49 (m, CH2O,
2 H C(5'), H C(4')), 5.72 (m, H C(3')), 6.55 (ꢀtꢁ, J ˆ 6.2, H C(1)), 7.00 (s, NH2); 7.34 ± 7.93 (4d, J ˆ 8.1,
MeC6H4). Anal. calc. for C29H30IN5O6 (671.5): C 51.87, H 4.50, N 10.43; found: C 52.07, H 4.51, N 10.36.
From the slower-migrating zone (cf. 7a/8), 8 was isolated as a colorless foam (640 mg, 18%).
3-Bromo-1-[2-deoxy-b-d-erythro-pentofuranosyl]-4-propoxy-1H-pyrazolo[3,4-d]pyrimidine-6-amine (9a).
A soln. of 7a (2.5 g, 4 mmol) in 0.1m NaOPr/PrOH (100 ml) was stirred for 1.5 h at 408. Then, the soln. was
adsorbed on silica gel and chromatographed (silica gel, column 12 Â 4 cm), A, then B): 9a (1.25 g, 81%).
Colorless needles . M.p.1808. TLC (silica gel, B): Rf 0.3. UV (MeOH): 256 (7500), 278 (9100). 1H-NMR
((D6)DMSO): 1.01 (t, J ˆ 7.4, Me); 1.77 (m, CH2); 2.18 (m, Ha C(2')); 2.68 (ꢀqꢁ, J ˆ 6.4, Hb C(2')); 3.35,
3.47 (m, 2 H C(5')); 3.77 (m, H C(4')); 4.34 (m, CH2O, H C(3')); 4.67 (t, J ˆ 5.5, OH C(5')); 5.22 (d, J ˆ
4.2; OH C(3')); 6.36 (ꢀtꢁ, J ˆ 6.2, H C(1')), 6.99 (s, NH2). Anal calc. for Cl3H18BrN5O4 (388.2): C 40.22,
H 4.67, N 18.04; found: C 40.15, H 4.73, N 18.10.
1-[2-Deoxy-b-d-erythro-pentofuranosyl]-3-iodo-4-propoxy-1H-pyrazolo[3,4-d]pyrimidin-6-amine
(9b).
As described for 9a, with 7b (2.5 g, 3.7 mmol) in 0.1m NaOPr/PrOH (100 ml, 2 h, 408): 9b (1.27 g, 78%).
Colorless needles. M.p. 1918. TLC (silica gel, B): Rf 0.3. UV (MeOH): 256 (7500), 278 (9100). 1H-NMR
((D6)DMSO): 1.1 (t, J ˆ 7.0, Me); 1.82 (m, CH2); 2.22 (m, Ha C(2')); 2.76 (ꢀqꢁ, J ˆ 6.4, Hb C(2')); 3.40,
3.52 (m, 2 H C(5')); 3.82 (m, H C(4')); 4.41 (m, CH2O, H C(3')); 4.73 (t, J ˆ 4.9, OH C(5')); 5.24 (d, J ˆ
3.7, OH C(3')); 6.37 (ꢀtꢁ, J ˆ 5.9, H C(1')), 6.96 (s, NH2). Anal. calc. for Cl3Hl8IN5O4 (435.2): C 35.88, H 4.17,
N 16.09; found: C 36.02, H 4.26, N 15.93.
4H-Pyrazolo[3,4-d]pyrimidin-4-ones 1 and 2. All anal. data were identical with those published earlier
[19].

122
Helvetica Chimica Acta ± Vol. 82 (1999)
REFERENCES
[1] a) W. Saenger, ꢀPrinciples of Nucleic Acid Structureꢁ, in ꢀSpringer Advanced Texts in Chemistryꢁ, Ed. C. R.
Cantor, Springer Verlag, New York ± Berlin ± Heidelberg ± Tokyo, 1984, p. 14 ± 17; b) ibid., p. 330; c) ibid.,
p. 73 ± 76; d) ibid., p. 17 ± 21; e) ibid., p. 23 ± 24; f) ibid., p. 106; g) ibid., p. 67.
[2] K. Kitamura, A. Wakahara, H. Mizuno, Y. Baba, K. Tomita, J. Am. Chem. Soc. 1981, 103, 3899.
[3] M. Sundaralingam, Biopolymers 1969, 7, 821; S. Arnott, D. W. L. Hukins, Nature (London) 1969, 224, 886;
R. H. Sarma, C.-H. Lee, F. E. Evans, N. Yathindra, M. Sundaralingam, J. Am. Chem. Soc. 1974, 96, 7337;
H. M. Berman, S. Neidle, R. K. Stodola, Proc. Natl. Acad. Sci. U.S.A. 1978, 5, 828.
[4] M. Sundaralingam, in ꢀProceedings of the 5th Jerusalem Symposium Quantum Chemistry and
Biochemistryꢁ, Eds. E. D. Bergmann and B. Ullman, Academic Press, New York, 1973, p. 417 ± 455.
[5] A. J. Kirby, ꢀThe Anomeric Effect and Related Stereoelectronic Effects at Oxygenꢁ, in ꢀReactivity and
Â
Structure Concepts in Organic Chemistryꢁ, Eds. K. Hafner, J.-M. Lehn, C. W. Rees, P. von Rague Schleyer,
B. M. Trost and R. Zahradnik, Springer Verlag, New York ± Berlin ± Heidelberg ± Tokyo, 1983, Vol. 5.
[6] J. Plavec, ꢀStudies on Stereoelectronic Effects in Nucleosides and Nucleotidesꢁ, Thesis, Uppsala University,
1995.
[7] W. Hillen, H. G. Gassen, Biochem. Biophys. Acta 1978, 518, 7; W. Uhl, J. Reiner, H. G. Gassen, Nucleic.
Acids Res. 1983, 11, 1167; W. Hillen, H. G. Gassen, Nucleic. Acids Res., Spec. Supply, 1978, 149.
[8] J. Plavec, W. Tong, J. Chattopadhyaya, J. Am. Chem. Soc. 1993, 115, 9734; J. Plavec, N. Garg, J.
Chattopadhyaya, J. Chem. Soc., Chem. Commun. 1993, 1011; J. Plavec, L. H. Koole, J. Chattopadhyaya,
Biochem. Biophys. Meth. 1992, 25, 253; L. H. Koole, H. M. Buck, A. Nyilas, J. Chattopadhyaya, Can. J.
Chem. 1987, 65, 2089; L. H. Koole, H. M. Buck, H. Bazin, J. Chattopadhyaya, Tetrahedron 1987, 43, 2989;
L. H. Koole, J. Plavec, H. Liu, B. R. Vincent, M. R. Dyson, P. L. Coe, R. T. Walker, G. W. Hardy, S. G.
Rahim, J. Chattopadhyaya, J. Am. Chem. Soc. 1992, 114, 9936; J. Plavec, C. Thibaudeau, G. Viswanadham,
C. Sund, J. Chattopadhyaya, J. Chem. Soc., Chem. Commun. 1994, 781; C. Thibaudeau, J. Plavec, K. A.
Watanabe, J. Chattopadhyaya, ibid. 1994, 537; C. Thibaudeau, J. Plavec, N. Garg, A. Papchikhin, J.
Chattopadhyaya, J. Am. Chem. Soc. 1994, 116, 4038; C. Thibaudeau, J. Plavec, J. Chattopadhyaya, ibid.
1994, 116, 6558; C. Thibaudeau, J. Plavec, J. Chattopadhyaya, ibid. 1994, 116, 8033; C. Thibaudeau, J.
Plavec, J. Chattopadhyaya, J. Org. Chem. 1996, 61, 266.
[9] H. Rosemeyer, F. Seela, J. Chem. Soc., Perkin Trans. 2 1997, 2341.
[10] H. Rosemeyer, M. Zulauf, N. Ramzaeva, G. Becher, E. Feiling, K. Mühlegger, I. Münster, A. Lohmann, F.
Seela, Nucleosides Nucleotides 1997, 16, 821.
[11] F. Seela, H. Thomas, Helv. Chim. Acta 1995, 78, 94.
[12] N. Ramzaeva, F. Seela, Helv. Chim. Acta 1996, 79, 1549.
[13] F. Seela, M. Zulauf, Chem.± Eur. J. 1998, 4, 1781.
[14] F. Seela, G. Becher, J. Chem. Soc., Chem. Commun. 1998, 2017.
[15] F. Seela, G. Becher, M. Zulauf, Nucleosides Nucleotides 1999, in press.
[16] F. Seela, N. Ramzaeva, M. Zulauf, Nucleosides Nucleotides 1997, 16, 963.
[17] W. K. Olson, R. D. Dasika, J. Am. Chem. Soc. 1976, 98, 5371.
[18] W. K. Olson, Proc. Natl. Acad. Sci. U.S.A. 1977, 74, 1775.
[19] F. Seela, G. Becher, Synthesis 1998, 2, 207.
[20] N. Ramzaeva, F. Seela, Helv. Chim. Acta 1995, 78, 1083.
[21] M. Hoffer, Chem. Ber. 1960, 93, 2777.
[22] F. Seela, M. Zulauf, G. Becher, Nucleosides Nucleotides 1997, 16, 305.
[23] P. Singh, D. J. Hodgson, J. Am. Chem. Soc. 1974, 96, 5276.
[24] S. Sprang, R. Scheller, D. Rohrer, M. Sundaralingam, J. Am. Chem. Soc. 1978, 100, 2867.
[25] J. D. Anderson, H. B. Cottam, S. B. Larson, L. D. Nord, G. R. Revankar, R. K. Robins, J. Heterocycl.
Chem. 1990, 27, 439.
[26] D. C. Ward, E. Reich, Ann. Rep. Med. Chem. 1969, 272.
[27] D. C. Ward, E. Reich, Proc. Natl. Acad. Sci. U.S.A 1968, 61, 1494.
[28] D. C. Ward, A. Cerami, E. Reich, G. Acs, L. Altwerger, J. Biol. Chem. 1969, 244, 3243.
[29] Entry 1: 6-thiopurine riboside, A. E. Shefter, J. Pharm. Sci. 1968, 57, 1157; Entry 2: tuberidin, J. Abola, M.
Sundaralingam, Acta Crystallogr., Sect. B 1973, 29, 697; Entry 3: dihydrouridine hemihydrate, structure A,
D. Suck, W. Saenger, K. Zeckmeister, Acta Crystallogr., Sect B 1972, 28, 596; Entry 4: dihydrouridine
hemihydrate structure B, ibid.; Entry 5: guanosine dihydrate, C. E. Bugg, R. E. Marsh, ibid. 1970, 26, 1089;
Entry 6: dihydrothymidine, J. Konnert, I. L. Karle, ibid. 1970, 26, 770; Entry 7: dihydrouridine, structure A,

Helvetica Chimica Acta ± Vol. 82 (1999)
123
M. Sundaralingam, S. T. Rao, J. Abola, J. Am. Chem. Soc. 1970, 93, 1089; Entry 8: dihydrouridine, structure
B, ibid.; Entry 9: inosine dihydrate, U. Thewalt, C. E. Bugg, R. E. Marsh, Acta Crystallogr., Sect B 1970, 26,
1089; Entry 10: 3-deazauridine, C. W. Schwalbe, W. Saenger, ibid. 1973, 29, 61; Entry 11: 5-hydroxyuridine,
U. Thewalt, C. E. Bugg, ibid. 1973, 29, 1393; Entry 12: 4-thiouridine, W. Saenger, K. H. Scheit, J. Mol. Biol.
1970, 50, 153; Entry 13: 6-thiopurine riboside, structure B, E. Shefter, J. Pharm. Sci. 1968, 57, 1157; Entry
14: N2,N2-dimethylguanosine, T. Brennan, C. Weeks, E. Shefter, S. T. Rao, M. Sundaralingam, J. Am.
Chem. Soc. 1972, 94, 8548; Entry 15: adenosine hydrochloride, K. Shikata, T. Ueki, T. Mitsui, Acta
Crystallogr., Sect B 1973, 29, 31; Entry 16: adenosine, T. F. Lai, R. E. Marsh, ibid. 1972, 28, 1982; Entry 17:
1-(b-d-arabinofuranosyl)uracil, P. Tollin, H. R. Wilson, D. W. Young, ibid. 1973, 29, 1641; Entry 18: 5-
chlorouridine, S. W. Hawkinson, C. L. Coulter, ibid., 1971, 27, 34; Entry 19: 1-(b-d-arabinofuranosyl)cy-
tosine hydrochloride, J. S. Sherfinski, R. E. Marsh, ibid., 1973, 29, 192; Entry 20: 5-chloro-2'-deoxyuridine,
D. W. Young, E. M. Morris, ibid., 1973, 29, 1259; Entry 21: thymidine, D. W. Young, P. Tollin, H. R. Wilson,
ibid. 1969, 25, 1423; Entry 22: 2,4-dithiouridine hydrate, G. Lin, M. Sundaralingam, ibid. 1971, 27, 961;
Entry 23: 2-thiocytidine dihydrate, G. H. Y. Lin, M. Sundaralingam, S. K. Akora, J. Am. Chem. Soc. 1971,
93, 1235; Entry 24: 2,4-dithiouridine hydrate, W. Saenger, D. Suck, Acta Crystallogr., Sect B 1971, 27, 1178;
Entry 25: cytidine; S. Furberg, C. Petersen, C. Romming, ibid. 1965, 20, 313; Entry 26: 5-nitrouridine, E.
Egert, H. J. Lindner, W. Hillen, H. G. Gassen, Nucleic Acids Res. 1977, 4, 929; Entry 27: uridine, E. A.
Green, R. D. Rosenstein, R. Shiono, D. J. Abraham, B. L. Trus, R. E. Marsh, Acta Crystallogr., Sect B 1975,
31, 102; Entry 28: 5-methyluridine hemihydrate, D. J. Hunt, E. Subramanian, ibid. 1969, 25, 2144; Entry 29:
5-methoxyuridine, W. Hillen, E. Egert, H. J. Lindner, H. Vorbrüggen, J. Carbohydr. Nucleosides
Nucleotides 1978, 5, 23; Entry 30: 5-hydroxyuridine, U. Thewalt, C. E. Bugg, Acta Crystallogr., Sect B
1973, 29, 1393; Entry 31: 5-(dimethylamino)uridine, E. Egert, H. J. Lindner, W. Hillen, H. G. Gassen, ibid.
1979, 35, 920; Entry 32: 5-aminouridine, E. Egert, H. J. Lindner, W. Hillen, H. G. Gassen, ibid. 1978, 34,
2204; Entry 33: 8-bromoguanosine dihydrate, C. E. Bugg, U. Thewalt, Biochem. Biophys. Res. Commun.
1969, 37, 623; Entry 34: 7-methylguanosine iodide trihydrate, structure A, Y. Yamagata, S. Fukumoto, K.
Hamada, T. Fujiwara, K.-I. Tomita, Nucleic Acids Res. 1983, 11, 6475; Entry 35: 7-methylguanosine,
structure B, ibid.; Entry 36: 8-chloroguanosine dihydrate, G. I. Birnbaum, P. Lassota, D. Shugar,
Biochemistry 1984, 23, 5048; Entry 37: 8-methylguanosine trihydrate, K. Hamada, I. Honda, S. Fujii, T.
Fujiwara, K.-I. Tomita, Acta Crystallogr., Sect.C 1985, 41, 1486; Entry 38: 8-iodoguanosine monohydrate, Y.
Sugawara, Y. Iimura, H. Iwasaki, H. Saito, J. Biomol. Struct. Dyn. 1994, 11, 721; Entry 39: guanosine
dihydrate, ibidi.; Entry 40: thymidine, A. N. Chekhlov, Zh. Strukt. Khim. 1995, 36, 178; Entry 41: (3'S,5'R)-
1-(2'-deoxy-3',5'-ethano-b-d-ribofuranosyl)thymine, M. Tarkoy, M. Bolli, B. Schweizer, C. Leumann,
Helv.Chim.Acta 1993, 76, 481; Entry 42: 5-bromo-2'-deoxycytidine monohydrate, J. N. Low, P. Tollin, P.
Whippy, Cryst. Struct. Commun. 1981, 10, 931; Entry 43: 5-bromo-2'-deoxycytidine, J. N. Low, P. Tollin, P.
Whippy, ibid. 1981, 10, 1369; Entry 44: cytidine (123 K), L. Chen, B. M. Craven, Acta Crystallogr., Sect.B
1995, 51, 1081; Entry 45: cytidine, S. Furberg, C. S. Petersen, C. Romming, Acta Crystallogr. 1965, 18, 313;
Entry 46: 2'-deoxycytidine hydrochloride, E. Subramanian, D. J. Hunt, Acta Crystallogr., Sect.B 1970, 26,
303; Entry 47: 2'-deoxycytidine, a-triclinic form, structure A, D. W. Young, H. R. Wilson, ibid. 1975, 31, 961;
Entry 48: 2'-deoxycytidine, a-triclinic form, structure B, ibid.; Entry 49: 2'-deoxy-5-methylcytidine, T. Sato,
Acta Crystallogr., Sect.C 1988, 44, 870; Entry 50: 2'-deoxy-5-(hydroxymethyl)cytidine, J. Li, S. V. P. Kumar,
A. L. Stuart, L. T. J. Delbaere, S. V. Gupta, ibid. 1994 50, 1837; Entry 51: 2'-deoxy-5-iodocytidine, F.
Ghiassy, J. N. Low, H. R. Wilson, Acta Crystallogr., Sect.B 1981, 37, 1921; Entry 52: 2'-deoxy-5-
ethylcytidine, S. Napper, A. L. Stuart, S. V. P. Kumar, V. S. Gupta, L. T. J. Delbaere, Acta Crystallogr.,
Sect.C 1995, 51, 96; Entry 55: 2'-deoxyguanosine, R. Marumoto, AIDS-Iyakuhin Kaihatsu-Kenkyu-Hokoku
(The Japanese Health Sciences Foundation) 1991, 3, 56; Entry 56: 2'-deoxytubercidin, V. Zabel, W. Saenger,
F. Seela, Acta Crystallogr., Sect.C 1987, 43, 131; Entry 57: 2'-deoxy-7-iodotubercidin, F. Seela, M. Zulauf, H.
Rosemeyer; H. Reuter, J. Chem. Soc., Perkin Trans.2 1996, 2373 Entry 58: 2'-deoxysangivamycin, T. Iimori,
T. Wakizaka, Y. Ohtsuka, S. Ohuchi, Y. Kodama, T. Oishi, Chem. Pharm. Bull. 1993, 41, 775; Entry 59: 7-
deaza-2'-deoxy-7-nitroadenosine, F. Seela, H. Rosemeyer, M. Zulauf, Y. Chen, G. Kastner, H. Reuter,
Liebigs Ann./ Recueil 1997, 2525; Entry 60: 7-deaza-2'-deoxy-8-methyl-guanosine, F. Seela, H. Rosemeyer,
M. Zulauf, Y. Chen, G. Kastner, H. Reuter, ibid. 1997, 2525; Entry 61: 6-azauridine, C. H. Schwalbe, W.
Saenger, J. Mol. Biol. 1973, 75, 129; Entry 62: formycin, P. Prusiner, T. Brennan, M. Sundaralingam,
Biochemistry 1973, 12, 1196; Entries 63 and 64: F. Seela, H. Debelak, H. Reuter, G. Kastner, I. A.
Mikhailopulo, Tetrahedron, in press.
[30] E. Egert, H. J. Lindner, W. Hillen, M. C. Böhm, J. Am. Chem. Soc. 1980, 102, 3707.
[31] A. Lo, E. Shefter, T. D. Cochran, J. Pharm. Sci. 1975, 64, 1707.

124
Helvetica Chimica Acta ± Vol. 82 (1999)
[32] F. Seela, H. Rosemeyer, M. Zulauf, Y. Chen, G. Kastner, H. Reuter, Liebigs Ann./Recueil 1997, 2525.
[33] U. Ellervik, G. Magnusson, J. Am. Chem. Soc. 1994, 116, 2340.
[34] F. Seela, H. Debelak, H. Reuter, G. Kastner, I. A. Mikhailopoulo, Tetrahedron, in press.
[35] I. A. Mikhailopoulo, E. N. Kalinichenko, T. L. Podkopaeva, T. Wenzel, H. Rosemeyer, F. Seela,
Nucleosides Nucleotides 1996, 15, 445; Thomas Wenzel, ꢀ Hoogsteen-Duplex DNA: Synthese und
Basenpaarung von 1-Desaza- und 1,3-Didesazaadenin Oligodesoxyribonucleotidenꢁ, Thesis, University of
Osnabrück, 1995, p. 17 ± 20.
[36] F. Seela, N. Ramzaeva, H. Rosemeyer, in ꢀ Hetarenesꢁ, Verlag Houben-Weyl, Vol. E 9b, ꢀBicyclic 6-Ring
Systems Each with One to Two N-Atoms ± Purinesꢁ, Weinheim, 1997, p. 403 J. A. Elvidge, J. R. Jones, C.
OꢁBrien, E. A. Evans, H. C. Sheppard, J. Chem. Soc., Perkin Trans. 2 1973, 1889; ibidem, Adv. Heterocycl.
Chem. 1974, 16, 1; J. R. Jones, S. E. Taylor, Chem. Soc. Rev. 1981, 10, 329.
[37] a) W. Saenger, Institut für Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14167 Berlin,
personal communication. b) J. van Wijk, C. Altona, ꢀPSEUROT 6.2 ± A Program for the Conformational
Analysis of the Five-Membered Ringsꢀ, University of Leiden, July 1993; C. A. G. Haasnoot, F. A. A. M. de
Leeuw, C. Altona, Tetrahedron 1980, 86, 2783.
[38] E. Westhof, O. Röder, I. Croneiss, H.-D. Lüdemann, Z. Naturforsch., C 1975, 30, 131.
[39] N. Ramzaeva, G. Becher, F. Seela, Synthesis 1998, 1327.
[40] F. Seela, M. Zulauf, H. Rosemeyer, H. Reuter, J. Chem. Soc., Perkin Trans. 2 1996, 2373.
[41] M. Ikehara, T. Tezuka, J. Am. Chem. Soc. 1973, 95, 4054.
[42] S. Uesugi, T. Tezuka, M. Ikehara, J. Am. Chem. Soc. 1976, 98, 969.
[43] F. Seela, G. Becher, unpublished results.
[44] A. Kumar, T. Maltseva, E. Zamaratski, X. Luo, J. Chattopadhyaya, Nucleosides Nucleotides 1999, in press.
[45] F. Seela, I. Münster, U. Löchner, H. Rosemeyer, Helv. Chim. Acta 1998, 81, 1139.
[46] F. Seela, K. Mersmann, B. Angerer, unpublished results.
[47] G. M. Sheldrick, ꢀProgram Package SHELXTLꢁ, Releases, Siemens Analytical X-Ray Instruments Inc.,
Madison (WI 53719), USA, 1994.
[48] F. Seela, H. Steker, Helv. Chim. Acta 1986, 69, 1602.
Received October 29, 1998