A family of hydrazone-based nucleosides for use in metal-mediated base pairs

Article abstract of DOI:10.1002/zaac.201300061

A new family of hydrazone-based nucleosides for use in metal-mediated base pairs was devised. The artificial nucleobases are derivatives of the papy ligand (papy = pyridinecarboxaldehyde-2′-pyridylhydrazone). By replacing the pendant pyridine moiety in papy by furan and thiophene, respectively, tridentate nucleosides with N, N, N-, N, N, O- and N, N, S-donor sites were obtained. As only a few transition metal complexes with pendant furan ligands have been reported, a model nucleobase for the N, N, O-donor nucleoside was synthesized. The molecular structures of its Cu²⁺, Ni²⁺, and Co ²⁺ complexes are reported. In all complexes, only weak M-O(furan) bonding is observed. The Co²⁺ complex displays a pentagonal bipyramidal coordination arrangement. In general, the structures of the metal complexes suggest that the respective nucleosides can be applied in metal-mediated base pairs. Copyright

Full text of DOI:10.1002/zaac.201300061

ARTICLE
DOI: 10.1002/zaac.201300061
A Family of Hydrazone-Based Nucleosides for Use in Metal-Mediated Base
Pairs
Christian Radunsky,[a] Dominik A. Megger,[a,b] Alexander Hepp,[a] Jutta Kösters,[a]
Eva Freisinger,[c] and Jens Müller*[a]
Dedicated to Professor Werner Uhl on the Occasion of His 60th Birthday
Keywords: Hydrazones; Coordination modes; DNA; Metal-mediated base pairs; Furan
Abstract. A new family of hydrazone-based nucleosides for use in model nucleobase for the N,N,O-donor nucleoside was synthesized.
metal-mediated base pairs was devised. The artificial nucleobases are The molecular structures of its Cu2+, Ni2+, and Co2+ complexes are
derivatives of the papy ligand (papy = pyridinecarboxaldehyde-2Ј-pyr-
idylhydrazone). By replacing the pendant pyridine moiety in papy by
furan and thiophene, respectively, tridentate nucleosides with N,N,N-,
N,N,O- and N,N,S-donor sites were obtained. As only a few transition
reported. In all complexes, only weak M–O(furan) bonding is ob-
served. The Co2+ complex displays a pentagonal bipyramidal coordina-
tion arrangement. In general, the structures of the metal complexes
suggest that the respective nucleosides can be applied in metal-medi-
metal complexes with pendant furan ligands have been reported, a ated base pairs.
are known for artificial metal-mediated base pairs.[6] Most of
Introduction
these comprise ligands with either nitrogen donor atoms (e.g.
imidazole,[4] triazole,[7] dipicolylamine,[8] 1-deazaadenine,[9]
1,3-dideazaadenine[10]), oxygen donor atoms (e.g. hydroxypyr-
idone[11]), or combinations thereof (e.g. salen,[12] hydroxyquin-
oline[13]). RNA-based metal-mediated base pairs have been re-
ported, too.[14] Only a limited number of reports exists on the
use of sulfur donor atoms, namely in the S,N,S-ligand 2,6-
bis(ethylthiomethyl)pyridine,[15] in the O,S-ligands mercap-
topyridone and hydroxylpyridinethione,[16] and in thiopyrimi-
dines.[17] The use of sulfur-containing ligands is particularly
interesting as it potentially allows the incorporation of softer
metal ions into metal-mediated base pairs. However, all metal-
mediated base pairs with sulfur-containing nucleosides that
have been reported to date inside a double helical context com-
prise silver(I) only. It is therefore highly important to study
systematically the effect of a gradually increasing softness of
the donor atoms within an otherwise unchanged system. We
therefore set out to devise a new class of artificial tridentate
ligand-based nucleosides with N,N,N-, N,N,O-, and N,N,S-do-
nor sets to elucidate this effect.
Mainly as a result of its superb self-assembly properties,
DNA is of utmost importance not only in the field of biochem-
istry. In fact, numerous applications for DNA have been devel-
oped that are independent of its biological origin. Examples
are its use as a breadboard for chemical reactions,[1] in asym-
metric catalysis,[2] or as a scaffold for functional molecules in
nanotechnology.[3] In the latter aspect, the site-specific decora-
tion of nucleic acids with metal ions (and hence with metal-
based functionality) represents another important area of re-
search. The most prominent method for the site-specific intro-
duction of metal ions is the formation of so-called metal-medi-
ated base pairs. In these base pairs, the hydrogen bonds be-
tween complementary nucleosides are formally replaced by co-
ordinative bonds. As a result, transition metal ions can be in-
corporated inside the double helix, aligned along the helical
axis.[4] Metal-mediated base pairs can in principle be formed
from entirely natural nucleosides,[5] but many more examples
* Prof. Dr. J. Müller
Fax: +49-251-83-36007
E-Mail: mueller.j@uni-muenster.de
[a] Institut für Anorganische und Analytische Chemie
Westfälische Wilhelms-Universität Münster
Corrensstr. 28/30
Results and Discussion
48149 Münster, Germany
[b] Current address:
To further explore the possible applications of nucleic acids
with metal-mediated base pairs, a family of novel hydrazone-
based artificial nucleosides was developed. Starting from 2-
hydrazinylpyridine (2a), the condensation with a furan-, pyr-
idine-, or thiophene-based aldehyde led to a variety of hydraz-
ones with N,N,N-, N,N,O-, or N,N,S-chelating abilities
(Scheme 1, R = H). Ligand 3a is commonly known as papy
Medizinisches Proteom-Center
Ruhr-Universität Bochum
Universitätsstr. 150
44801 Bochum, Germany
[c] Institute of Inorganic Chemistry
University of Zurich
Winterthurerstr. 190
8057 Zurich, Switzerland
Z. Anorg. Allg. Chem. 2013, 639, (8-9), 1621–1627
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
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J. Müller et al.
ARTICLE
(pyridinecarboxaldehyde-2Ј-pyridylhydrazone). Accordingly,
To prohibit (or at least to slow down the rate of) a nucleo-
we have dubbed ligands 3b and 3c fapy (derived from furan) philic attack of a water molecule at the imino carbon atom, a
and tapy (derived from thiophene), respectively.
second series of hydrazone-based nucleosides was synthesized.
In these nucleosides, the position at the imino carbon is steri-
cally blocked by a methyl group (R = CH3 in Scheme 1 and
Scheme 2). This was achieved by replacing the aldehyde in the
condensation reaction by the respective methyl ketone. As a
result, hydrazones 4a–4c and nucleosides 6a–6c were ob-
tained. These nucleosides proved to be much more hydrolyti-
cally stable: In methanol containing 15% D2O, no decomposi-
tion was detected even after one day. This increased hydrolytic
stability is important for an application in automated DNA
synthesis. Hence, the methylated nucleosides represent promis-
ing building blocks for new metal-mediated base pairs.
Typically, model nucleobases are used to investigate the
metal-binding behavior of nucleosides. In these model nucleo-
bases, the sugar moiety is formally replaced by an alkyl group.
As a result, the metal complexes have much simpler NMR
spectra and, more importantly, they crystallize more easily.
The alkylation prevents the nitrogen atom that is originally
involved in the glycosidic bond to participate in any metal
binding.[18a] In the natural nucleobases, this leads to N9-alkyl-
ated purine and N1-alkylated pyrimidine bases. Model nucleo-
bases have been successfully applied in previous structural
studies on metal-mediated base pairs.[18b–e]
Scheme 1. Synthesis of hydrazones 3a (papy, RЈ = pyridine-2-yl), 3b
(fapy, RЈ = furan-2-yl), and 3c (tapy, RЈ = thiophene-2-yl) from 2-
hydrazinylpyridine (2a) via condensation reaction with the respective
aldehyde (R = H). Reaction with the respective methyl ketone results
in hydrazones 4a, 4b, and 4c.
These ligands were incorporated as artificial nucleobases
into hydrazone-based nucleosides via reaction with Hoffer’s
chloro sugar (Scheme 2).
In the presented study, we investigated the metal-binding
behavior of a model nucleobase for the furan-containing nucleo-
side 5b in more detail. This particular ligand was chosen be-
cause only little data are available regarding transition metal
complexes of ligands with pendant furan rings.[19] The synthe-
sis of model nucleobase 7 (Scheme 3) followed the procedure
detailed in Scheme 1. However, it started from 2-(1-methylhy-
drazin-1-yl)pyridine (2b) rather than 2-hydrazinylpyridine
(2a). The reaction of 7 with Cu2+, Ni2+, and Co2+ yielded the
respective metal complexes, whose molecular structures were
determined by single-crystal X-ray diffraction analyses. For an
application in metal-mediated base pairs, the complexes should
ideally be planar, to allow stacking interactions with neigh-
boring nucleobases. Additional axial coordination by labile li-
gands is not necessarily of any disadvantage, as it indicates
that weak metal–metal interactions between consecutive metal-
mediated base pairs might be possible.
Scheme 2. Synthesis of hydrazone-based artificial nucleosides
(a: RЈ = pyridine-2-yl; b: RЈ = furan-2-yl; c: RЈ = thiophene-2-yl).
Initial investigations revealed that the papy nucleoside with
N,N,N-donor capability (5a) is rather unstable under aqueous
conditions, showing a decomposition by 50% already within
less than 5 h (Figure 1). A change to other polar solvents such
as methanol slightly increased the hydrolytic stability, albeit
not to a satisfactory extent.
Scheme 3. Chemical representation of model nucleobase 7.
Reaction of 7 with CuCl2 gave [Cu(7)Cl2] (8). Figure 2
shows the molecular structure of 8, and Table 1 lists relevant
bond lengths and angles. As can be seen, the metal complex
is not planar. Cu1 is coordinated by two nitrogen atoms with
bond lengths slightly below 2 Å and by two chlorido ligands
with bond lengths in the order of 2.20–2.25 Å. While the
Cu–N distances are in the normal range, the Cu–Cl bonds are
rather short. The shorter Cu–Cl distance is found for the equa-
Figure 1. Decomposition of papy nucleoside 5a in different solvents
as monitored by H NMR spectroscopy (• = D2O; ᭿ = CD3OD).
1
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A Family of Hydrazone-Based Nucleosides
Table 1. Relevant bond lengths /Å and angles /° in the molecular structures of compounds 8 and 9a. For comparison, selected bond lengths and
angles are also given for compound 10.
Bond, anglea)
8
9a
10
M–N1p
M–N2h
1.9780(16)
1.9960(15)
2.8519(15)
2.201(6)
2.2542(5)
–
79.66(6)
102.99(18)
127.94(5)
–
2.0092(14)
2.0707(13)
2.7504(14)
2.3339(5)
2.3378(5)
2.0565(12)
78.44(5)
102.93(4)
100.58(4)
93.46(5)
2.0398(12)
2.1533(11)
2.7667(11)
–
–
–
76.16(5)
–
–
–
M–O1f
M–Cl1b)
M–Cl2
M–O2
N1p–M–N2h
N1p–M–Cl1b)
N1p–M–Cl2
N1p–M–O2
N1p–M–O1f
N2h–M–Cl1
Cl1–M–Cl2b)
Cl1–M–O2
141.91(6)
149.19(15)
103.11(17)
–
146.64(5)
173.73(4)
93.361(17)
89.34(4)
142.58(4)
–
–
–
a) 8: M = Cu1, 9a: M = Ni1, 10: M = Co1. b) 8: Cl1 ϵ Cl1a.
torial chlorido ligand. The furan ligand is oriented in a way N1p–Ni1–N2h, N2h–Ni1–O1f, O1f–Ni1–Cl1, and Cl1–Ni1–
that an additional weak Cu1–O1f interaction is feasible. The N1p amounts to 359.33(9)°, thereby indicating the planarity of
respective distance amounts to 2.8519(15) Å and is therefore the tridentate ligand in combination with Cl1.
significantly longer than a typical Cu–O bond. Previously,
Cu–O bond lengths in copper complexes with pendant furan
ligands have been reported up to 2.595 Å.[20] Nonetheless, by
applying the van der Waals radii reported for copper (1.4 Å)
and oxygen (1.52 Å),[21] a weak bonding interaction between
Cu1 and O1f can be concluded for compound 8.
Figure 3. Molecular structure of [Ni(7)Cl2(DMSO)]·DMSO (9a). Hy-
drogen atoms and the non-coordinating DMSO molecule are omitted
for clarity. Thermal ellipsoids are drawn at a 30% probability level.
Reaction of 7 with Co(NO3)2·6H2O gave [Co(7)(NO3)2-
(H2O)] (10). Figure 4a shows the molecular structure of 10.
Figure 2. Molecular structure of [Cu(7)Cl2] (8). Hydrogen atoms are
Relevant bond lengths and angles are listed in Table 2. In 10,
omitted for clarity. Thermal ellipsoids are drawn at a 30% probability
the cobalt ion adopts an unusual pentagonal bipyramidal struc-
level.
ture (Figure 4b). One aqua ligand and one monodentate nitrato
Reaction of 7 with NiCl2·6H2O gave [Ni(7)Cl2] (9). ligand bind in the axial positions. The O3–Co1–O1a angle
Recrystallization of 9 from DMSO in an atmosphere of meth- amounts to 154.42(4)°, indicating a non-perfect bipyramid. A
anol gave [Ni(7)Cl2(DMSO)]·DMSO (9a). Figure 3 shows the bidentate nitrato ligand and the three donor sites from ligand
molecular structure of 9a. Relevant bond lengths and angles 7 are responsible for the pentagonal coordination. The sum
are listed in Table 1. In 9a, the central nickel ion adopts a of the inner angles N1p–Co1–N2h, N2h–Co1–O1f, O1f–Co1–
distorted octahedral coordination arrangement. The coordina- O2b, O2b–Co1–O2a, and O2a–Co1–N1p amounts to
tion sites on the axis oriented perpendicular to the tridentate 360.3(1)°, showing the perfect planarity of the pentagonal
ligand are occupied by one DMSO and one chlorido ligand. plane. With Co–O bond lengths of 2.1433(11) Å and
The DMSO ligand coordinates by its oxygen atom. As the sum 2.3416(11) Å, the bidentate nitrato ligand binds in a slightly
of the van der Waal radii of nickel (1.63 Å) and oxygen asymmetric fashion. Applying the criteria proposed by
(1.52 Å) is significantly larger than the observed Ni1–O1f dis- Driessen and co-workers,[22] the bidentate binding mode can
tance [2.7504(14) Å], a bonding interaction between Ni1 and be confirmed. The Co1–O1f distance in 10 amounts to
O1f can be concluded. Again, this bond is longer than pre- 2.7667(11) Å. Similar to what has already been concluded for
viously reported Ni–O bonds in nickel complexes with pendant compounds 8 and 9a, this distance suggests a weak bonding
furan ligands (2.202–2.358 Å).[19] The sum of the inner angles interaction.
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J. Müller et al.
ARTICLE
Scheme 4. Chemical representation of a potential metal-mediated base
pair formed from nucleoside 6b and an imidazole nucleoside.
stable against hydrolysis. They hence represent feasible build-
ing blocks for DNA.
A model nucleobase 7 was synthesized, representing the
furan-containing artificial nucleoside. The molecular structures
of the metal complexes of 7 with Cu2+ (8), Ni2+ (9a), and
Co2+ (10) clearly indicate that the family of hydrazone-based
nucleosides should be capable of forming planar metal-medi-
ated base pairs.
The complex [Cu(7)Cl2] (8) shows a strong distortion from
planarity. Moreover, it contains the weakest M–O1f bond be-
tween the central metal atom and the furan ring. Hence, out of
the three transition metals under investigation, Cu2+ appears to
be the least favored one in terms of applicability in a metal-
mediated base pair. In contrast, the octahedral complex
[Ni(7)Cl2(DMSO)]·DMSO (9a) indicates that Ni2+ might be a
good candidate for the central metal ion in a metal-mediated
base pair containing one of the hydrazone nucleosides. When
incorporated into a DNA duplex, the two axial ligands
(DMSO, Cl–) could either be substituted by donor sites from
within the DNA strand (a related finding has been reported
previously)[24] or could be replaced by a weak axial metal–
metal interaction between neighboring artificial base pairs. The
same reasoning applies for the pentagonal bipyramidal
[Co(7)(NO3)2(H2O)] (10) with the axially coordinating aqua
and nitrato ligands. Moreover, the pentagonal coordination en-
vironment in this complex nicely demonstrates the relatively
large space available for the monodentate complementary nu-
cleoside. In contrast to other combinations of tridentate and
monodentate ligands, in which a steric clash prohibits the for-
mation of entirely planar complexes,[8,18c] the furan-containing
systems are therefore more promising in terms of their applica-
bility in planar metal-mediated base pairs.
Figure 4. (a) Molecular structure of [Co(7)(NO3)2(H2O)] (10). Hydro-
gen atoms are omitted for clarity. (b) Distorted pentagonal bipyramidal
coordination environment of Co1. Thermal ellipsoids are drawn at a
30% probability level.
Table 2. Relevant bond lengths /Å and angles /° in the molecular struc-
ture of compound 10.
Co1–N1p
Co1–N2h
Co1–O1f
Co1–O1a
Co1–O2a
Co1–O2b
Co1–O3
2.0398(12)
2.1533(11)
2.7667(11)
2.0537(10)
2.1433(11)
2.3416(11)
2.0653(11)
N1p–Co1–N2h
N1p–Co1–O3
N1p–Co1–O1a
N1p–Co1–O2a
N1p–Co1–O1f
O3–Co1–O1a
O3–Co1–O2a
76.16(5)
96.35(4)
109.08(4)
95.46(4)
142.58(4)
154.42(4)
93.96(4)
Conclusions
A new family of hydrazone-based nucleosides for use in
metal-mediated base pairs was synthesized and characterized.
Experimental Section
Depending on the identity of the pendant heterocyclic ligand, General: The para-toluoyl-protected 2-deoxy-d-ribose (1) as well as
2-hydrazinylpyridine (2a) and 2-(1-methylhydrazin-1-yl)pyridine (2b)
were synthesized according to published procedures.[25] 1H and 13C
NMR spectra were recorded with Bruker Avance (I) 400 and Avance
(III) 400 spectrometers with an internal standard relative to TMS (δ /
ppm = 0) for measurements in CDCl3. In case of using [D6]DMSO
and [D4]methanol the residual solvent signal was used for internal
standards. For a complete assignment of the nucleosides, 1H,1H-
ROESY, 1H,13C{1H}-HSQC, 1H,13C{1H}-HMBC and 1H,1H-gCOSY
experiments were performed. Mass spectra were recorded with a
Bruker Reflex IV (MALDI-TOF) and with a Bruker Daltonics Micro
the artificial nucleobases provide an N,N,N-, N,N,O-, or
N,N,S-donor set. To be applied in the formation of metal-medi-
ated base pairs, the tridentate hydrazone nucleoside will be
placed in one strand and a monodentate nucleoside (e.g. an
azole nucleoside)[23] in the complementary strand (Scheme 4).
The first-generation nucleoside 5a showed a relatively fast
decomposition in aqueous solution, rendering it inadequate for
an application in metal-mediated base pairs. The second-gener-
ation nucleosides 6a–6c, all carrying a methyl substituent at
the imino carbon of the hydrazone moiety, were much more TOF spectrometer (EI, ESI).
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A Family of Hydrazone-Based Nucleosides
Synthesis of the Hydrazones (3a, 3b, 3c): To a solution of 2a in Synthesis of the Nucleosides (5a, 5b, 5c): To a solution of the hydraz-
EtOH (40 mL) were added 0.5 equivalents of acetic acid as catalyst one (3a, 3b, 3c) in CH3CN (50 mL) 1.1 equivalents of NaH (60%)
and one equivalent of the pyridine- (3a), furan- (3b) or thiophene- were added. The resulting suspension was stirred for 40 min. Over the
substituted (3c) aldehyde. The reaction mixture was stirred for 45 min
duration of 90 min, 1.1 equivalents of 1 were added in 4 portions. The
at 55 °C. After reducing the reaction volume to the half, H2O (10 mL)
suspension was stirred for further 3 h at ambient temperature, filtered,
was added, and the yellow-orange product crystallized overnight at and washed with CH2Cl2 (120 mL). The filtrate was evaporated to
–26 °C. The product was filtered and dried (40 °C). 3a: Yield 80%.
1H NMR (CDCl3): δ = 10.07 (s, 1 H, NH); 8.56 (dd, 1 H, H6**); 8.21
(dd, 1 H, H6*); 7.99 (dd, 1 H, H3**); 7.92 (s, 1 H, H3); 7.68 (ddd, 1
H, H4*); 7.62 (ddd, 1 H, H4**); 7.42 (dd, 1 H, H3*); 7.18 (ddd, 1 H,
H5**); 6.81 (ddd, 1 H, H5*). 13C NMR (CDCl3): δ = 156.8 (C2**);
dryness and re-dissolved in methanol (60 mL). After the addition 2.3
equivalents of K2CO3 the suspension was stirred for 20 h at ambient
temperature. To the clear solution CH2Cl2 (50 mL) and H2O (25 mL)
were added. After separation of the organic layer, the aqueous layer
was washed with CH2Cl2 (3ϫ30 mL). The combined organic layers
154.4 (C2*); 149.3 (C6**); 147.3 (C6*); 139.3 (C3); 138.3(C4*); were washed with brine (15 mL), dried (Na2SO4), and the solvents
136.2 (C4**); 122.9 (C5**); 119.7 (C3**); 116.2 (C5*); 107.7 (C3*). evaporated to dryness. The crude product was purified by column
C11H10N4 (198.0905): C 66.8 (calcd. 66.7); H 5.1 (calcd. 5.1); N 28.3 chromatography (SiO2, 0.035–0.070 mm, 60 Å), 5a: CH2Cl2
(calcd. 28.3)%. MALDI-TOF-MS: m/z = 198 (M+: 198). 3b: Yield
70%. H NMR (CDCl3): δ = 9.30 (s, 1 H, NH); 8.13 (dd, 1 H, H6*);
7.70 (s, 1 H, H3); 7.60 (ddd, 1 H, H4*); 7.48 (dd, 1 H, H5**); 7.36
(ddd, 1 H, H5*); 6.78 (dd, 1 H, H3*); 6.60 (dd, 1 H, H3**); 6.46 (ddd,
1 H, H4**). 13C NMR (CDCl3): δ = 156.7 (C2*); 150.3 (C2**); 146.9
(18):MeOH (1):Et3N (1), 5b: CH2Cl2 (18):MeOH (1): Et3N (1), 5c:
CH2Cl2 (20):MeOH (1):Et3N (1). 5a: Yield 76%. 1H NMR
([D6]DMSO): δ = 8.56 (dd, 1 H, H6**); 8.33 (dd, 1 H, H6*); 8.32 (s,
1 H, H3); 7.95 (d, 1 H, H3**); 7.83 (ddd, 1 H, H4**); 7.81 (ddd, 1
H, H4*); 7.54 (d, 1 H, H3*); 7.33 (ddd, 1 H, H5**); 7.06 (ddd, 1 H,
1
(C6*); 143.4 (C5**); 138.3 (C4*); 129.5 (C3); 115.8 (C3**); 111.7 H5*); 6.80 (pt, 1 H, H1Ј); 5.24 (s, 1 H, 3Ј-OH); 4.87 (s, 1 H, 5Ј-OH);
(C5*); 110.2 (C4**); 107.8 (C3*). C10H9N3O (187.0746): C 64.0
(calcd. 64.2); H 4.9 (calcd. 4.9); N 22.3 (calcd. 22.5)%. MALDI-
TOF-MS: m/z = 188 (M+H+: 188). 3c: Yield 75%. 1H NMR (CDCl3):
4.31 (m, 1 H, H3Ј); 3.70 (m, 1 H, H4Ј); 3.62–3.52 (m, 2 H, H5Ј, H5ЈЈ);
2.66 (m, 1 H, H2Ј); 1.91 (m, 1 H, H2ЈЈ). 13C NMR ([D6]DMSO): δ =
156.3 (C2*); 154.4 (C2**); 149.2 (C6**); 147.1 (C6*); 140.9 (C3);
δ = 9.35 (s, 1 H, NH); 8.13 (dd, 1 H, H6*); 7.96 (s, 1 H, H3); 7.61 138.5 (C4*); 136.5 (C4**); 123.2 (C5*); 119.1 (C3*); 118.1 (C5**);
(ddd, 1 H, H4*); 7.35 (ddd, 1 H, H5**); 7.28 (dd, 1 H, H3**); 7.13
112.9 (C3**); 86.0 (C4Ј); 85.9 (C1Ј); 70.2 (C3Ј); 61.5 (C5Ј); 34.2
(ddd, 1 H, H4**); 7.02 (dd, 1 H, H5*); 6.78 (dd, 1 H, H3*). 13C NMR (C2Ј). C16H18N4O3·0.3H2O: C 60.1 (calcd. 60.0); H 5.9 (calcd. 5.9);
(CDCl3): δ = 156.8 (C2*); 146.9 (C6*); 140.2 (C2**); 138.2 (C4*); N 17.1 (calcd. 17.5)%. ESI-MS: m/z = 337.1272 (M+Na+: 337.1277).
133.9 (C3); 127.3 (C5**); 127.2 (C4**); 126.4 (C3**); 115.6 (C5*); 5b: Yield: 63%. H NMR ([D6]DMSO): δ = 8.50 (s, 1 H, H3); 8.25
1
107.7 (C3*). C10H9N3S (203.0517): C 59.2 (calcd. 59.1); H 4.4 (calcd. (dd, 1 H, H6*), 7.77 (dd, 1 H, H5**); 7.73 (ddd, 1 H, H4*); 7.38 (dd,
4.5); N 20.7 (calcd. 20.7)%. MALDI-TOF-MS: m/z = 204 (M+H+: 1 H, H3*); 6.94 (ddd, 1 H, H5*); 6.94 (pt, 1 H, H1Ј); 6.73 (dd, 1 H,
204).
H3**); 6.60 (ddd, 1 H, H4**); 5.20 (s, 1 H, OH); 4.96 (s, 1 H, OH);
4.31 (dt, 1 H, H3Ј); 3.68 (dd, 1 H, H4Ј); 3.61–3.56 (m, 2 H, H5Ј, H5ЈЈ);
Synthesis of the Methylated Hydrazones (4a, 4b, 4c): To a solution 2.52 (dd, 1 H, H2Ј); 1.82 (dd, 1 H, H2ЈЈ). 13C NMR ([D6]DMSO): δ
of 2a in EtOH (50 mL) were added 0.5 equivalents of acetic acid and = 156.8 (C2*); 150.5 (C2**); 146.9 (C6*); 144.0 (C5**); 138.2 (C4*);
one equivalent of the pyridine- (4a), furan- (4b) or thiophene-substi-
tuted (4c) ketone. The reaction mixture was stirred for 70 min at 55 °C.
134.6 (C3); 116.8 (C5*); 111.8 (C4**); 111.6 (C3**); 111.3 (C3*);
85.8 (C4Ј); 85.6 (C1Ј); 69.8 (C3Ј); 60.9 (C5Ј); 33.8 (C2Ј). C15H17N3O4
The volume was reduced to half, and H2O (15 mL) was added. The (303.1219): C 59.0 (calcd. 59.4); H 5.7 (calcd. 5.7); N 13.5 (calcd.
solution was flash-frozen in liquid nitrogen, and the product crys-
tallized at –26 °C overnight. 4a: Yield 68%. H NMR (CDCl3): δ =
8.16 (s, 1 H, NH); 8.11 (dd, 1 H, H6**); 7.64 (dd, 1 H, H6*); 7.59
(dd, 1 H, H3**); 7.46 (ddd, 1 H, H4*); 7.36 (ddd, 1 H, H4**); 6.78
(dd, 1 H, H3*); 6.65 (ddd, 1 H, H5*); 6.45 (ddd, 1 H, H5**); 2.21 (s,
13.8)%. ESI-MS: m/z = 326.1112 (M+Na+: 326.1117). 5c: Yield 61%.
1H NMR ([D6]DMSO): δ = 8.84 (s, 1 H, H3); 8.25 (dd, 1 H, H6*),
7.74 (ddd, 1 H, H4*); 7.57 (dd, 1 H, H5**); 7.30 (ddd, 1 H, H5*);
7.30 (dd, 1 H, H3**); 7.11 (ddd, 1 H, H4**); 6.93 (dd, 1 H, H3*) 6.93
(pt, 1 H, H1Ј); 5.20 (s, 1 H, OH); 5.00 (s, 1 H, OH); 4.32 (dt, 1 H,
1
3 H, CH3). 13C NMR (CDCl3): δ = 156.8 (C2**); 152.8 (C2*); 147.2 H3Ј); 3.69 (dd, 1 H, H4Ј); 3.62–3.57 (m, 2 H, H5Ј, H5ЈЈ); 2.52 (dd, 1
(C6**); 144.8 (C6*); 142.9 (C3); 139.3 (C4*); 137.8 (C4**); 115.2 H, H2Ј); 1.83 (dd, 1 H, H2ЈЈ). 13C NMR ([D6]DMSO): δ = 156.7
(C5**); 111.5 (C3**); 108.7 (C5*); 108.4 (C3*); 12.6 (CH3). (C2*); 147.0 (C6*); 140.8 (C2**); 140.6 (C3); 138.2 (C4*); 129.0
C12H12N4 (212.1062): C 67.7 (calcd. 67.9); H 5.6 (calcd. 5.7); N 26.2 (C3**); 127.6 (C4**); 127.3 (C5**); 116.7 (C5*); 111.0 (C3*); 85.8
(calcd. 26.4)%. MALDI-TOF-MS: m/z = 213 (M+H+: 213). 4b: Yield (C4Ј); 85.7 (C1Ј); 69.9 (C3Ј); 61.0 (C5Ј); 34.0 (C2Ј). C15H17N3O3S
1
62%. H NMR (CDCl3): δ = 9.73 (s, 1 H, NH); 7.95 (dd, 1 H, H6*);
(319.0991): C 56.2 (calcd. 56.4); H 5.4 (calcd. 5.4); N 13.0 (calcd.
7.64 (ddd, 1 H, H4*); 7.48 (dd, 1 H, H5**); 7.46 (dd, 1 H, H3**); 13.2)%. ESI-MS: m/z = 342.0883 (M+Na+: 342.0888).
6.68 (ddd, 1 H, H5*); 6.66 (dd, 1 H, H3*); 6.45 (ddd, 1 H, H4**);
2.28 (s, 3 H, CH3). 13C NMR (CDCl3): δ = 156.8 (C2*); 152.9 (C2**); Synthesis of the Methylated Nucleosides (6a, 6b, 6c): Compounds
144.6 (C6*); 143.0 (C5**); 140.0 (C3); 138.0 (C4*); 115.1 (C3**); 6a–6c were synthesized in analogy to nucleosides 5a–5c. After ad-
112.5 (C5*); 108.8 (C4**); 108.5 (C3*); 12.7 (CH3). C11H11N3O·0.5
dition of 1 to a solution of 4a–4c in CH3CN, the reaction mixture was
CH3COOH: C 62.5 (calcd. 62.3); H 5.7 (calcd. 5.7); N 18.4 (calcd. stirred for 5 h at ambient temperature. The deprotection with K2CO3
18.2)%. MALDI-TOF-MS: m/z = 202; (M+H+: 202). 4c: Yield 50%. required 26 h. The crude product was purified by column chromatog-
1H NMR (CDCl3): δ = 9.31 (s, 1 H, NH); 7.99 (dd, 1 H, H6*); 7.63
raphy (SiO2, 0.035–0.070 mm, 60 Å), 6a: CH2Cl2 (18):MeOH
(ddd, 1 H, H4*); 7.42 (dd, 1 H, H5**); 7.24 (dd, 1 H, H3**); 7.19 (2):Et3N (1), 6b: CH2Cl2 (18):MeOH (1):Et3N (1), 6c: CH2Cl2
1
(ddd, 1 H, H4**); 7.00 (ddd, 1 H, H5*); 6.76 (dd, 1 H, H3*); 2.32 (s,
(18):MeOH (1):Et3N (1). 6a: Yield 56%. H NMR ([D6]DMSO): δ =
3 H, CH3). 13C NMR (CDCl3): δ = 156.7 (C2*); 146.6 (C2**); 144.6 8.68 (dd, 1 H, H6**); 8.24 (dd, 1 H, H6*); 8.20 (d, 1 H, H3**); 7.94
(C6*); 140.1 (C5**); 138.5 (C3); 127.1 (C4*); 126.4 (C3**); 124.7 (ddd, 1 H, H4**); 7.59 (ddd, 1 H, H4*); 7.53 (d, 1 H, H3*); 6.86 (ddd,
(C5*); 115.6 (C4**); 108.0 (C3*); 13.0 (CH3). C11H11N3S (217.0674):
C 60.5 (calcd. 60.8); H 5.1 (calcd. 5.1); N 19.1 (calcd. 19.3)%.
MALDI-TOF-MS: m/z = 218 (M+H+: 218).
1 H, H5**); 6.62 (pt, 1 H, H1Ј); 6.55 (ddd, 1 H, H5*); 5.03 (s, 1 H,
3Ј-OH); 4.55 (s, 1 H, 5Ј-OH); 4.14 (m, 1 H, H3Ј); 3.65 (m, 1 H, H4Ј);
3.44–3.38 (m, 2 H, H5Ј, H5ЈЈ); 2.24 (m, 1 H, H2Ј); 2.15 (s, 3 H, CH3);
Z. Anorg. Allg. Chem. 2013, 1621–1627
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.zaac.wiley-vch.de
1625

J. Müller et al.
ARTICLE
1.96 (m, 1 H, H2ЈЈ). 13C NMR ([D6]DMSO): δ = 171.7 (C3); 156.9 7.46 (dd, 1 H, H5*); 6.78 (dd, 1 H, H3**); 6.61 (dd, 1 H, H3*); 6.46
(C2*); 154.5 (C2**); 148.9 (C6**); 147.8 (C6*); 137.8 (C4*); 136.8 (dd, 1 H, H4**); 3.61 (s, 3 H, CH3). 13C NMR (CDCl3): δ = 157.2
(C4**); 125.0 (C5**); 120.8 (C3**); 116.0 (C5*); 110.2 (C3*); 89.9 (C2*); 151.7 (C2**); 146.4 (C6*); 142.7 (C4**); 137.8 (C4*); 124.9
(C4Ј); 86.0 (C1Ј); 70.9 (C3Ј); 62.7 (C5Ј); 45.7 (C2Ј); 15.8 (CH3). (C3); 115.6 (C5*); 111.6 (C4**); 110.2 (C3**); 108.8 (C3*); 29.5
C17H20N4O3 (328.1535): C 61.9 (calcd. 62.2); H 6.1 (calcd. 6.1); N (CH3). C11H11N3O (201.0902): C 65.5 (calcd. 65.7); H 5.4 (calcd. 5.5);
16.6 (calcd. 17.1)%. ESI-MS: m/z = 351.1438 (M+Na+: 351.1423).
6b: Yield 49%. 1H NMR ([D4]Methanol): δ = 7.67 (dd, 1 H, H6*),
7.65 (dd, 1 H, H5**); 7.32 (ddd, 1 H, H4*); 7.11 (dd, 1 H, H3*); 6.73
(ddd, 1 H, H5*); 6.53 (dd, 1 H, H3**); 6.20 (ddd, 1 H, H4**); 6.03
(pt, 1 H, H1Ј); 5.05 (s, 1 H, OH); 4.89 (s, 1 H, OH); 4.30 (dt, 1 H,
H3Ј); 4.28 (dd, 1 H, H4Ј); 3.39–3.18 (m, 2 H, H5Ј, H5ЈЈ); 2.65 (dd, 1
H, H2Ј); 2.22 (s, 3 H, CH3); 2.00 (dd, 1 H, H2ЈЈ). 13C NMR ([D4]Me-
thanol): δ = 155.1 (C2*); 152.1 (C2**); 146.4 (C6*); 143.7 (C3); 138.7
(C4*); 138.2 (C4**); 115.1 (C5*); 112.3 (C3*); 111.0 (C5**); 107.1
(C3**); 86.3 (C4Ј); 84.5 (C1Ј); 71.8 (C3Ј); 62.2 (C5Ј); 40.9 (C2Ј);
13.3 (CH3). C16H19N3O4 · 0.5 MeOH: C 59.3 (calcd. 59.4); H 6.3
(calcd. 6.4); N 12.6 (calcd. 12.6)%. ESI-MS: m/z = 340.1268 (M+Na+:
N 20.6 (calcd. 20.9)%. ESI-MS: m/z = 202.0980 (M+H+: 202.0980).
Synthesis of [Cu(7)Cl2] (8): The N,N,O-ligand (120.0 mg,
7
597 μmol) was dissolved in EtOH (10 mL). A solution of CuCl2·2 H2O
(100.8 mg, 598 μmol) in EtOH (10 mL) was added slowly. The re-
sulting suspension was stirred for 2 h at ambient temperature. The
solid was filtered off, washed with Et2O, and dried at 40 °C. The prod-
uct was obtained in 60% yield (120.2 mg, 360 μmol).
C11H11Cl2CuN3O·0.25H2O: C 38.8 (calcd. 38.8); H 3.2 (calcd. 3.4); N
12.3 (calcd. 12.4)%. ESI-MS: m/z = 298.9882 (M+–Cl: 298.9887). X-
ray: Single crystals of 8 were obtained by crystallizing the compounds
from methanol in an atmosphere of Et2O.
1
340.1273). 6c: Yield 55%. H NMR ([D4]Methanol): δ = 7.80 (dd, 1
Synthesis of [Ni(7)Cl2] (9): The N,N,O-ligand 7 (99.2 mg, 492 μmol)
was dissolved in MeOH (8 mL). A solution of NiCl2·6H2O (117.0 mg,
492 μmol) in MeOH (2 mL) was added slowly. The resulting suspen-
sion was refluxed at 80 °C for 2 h. The solid was filtered off and
washed with cold Et2O. After drying at 40 °C, the product was ob-
tained in 72% yield (118 mg, 357 μmol). C11H11Cl2CuN3O·0.25H2O:
C 39.9 (calcd. 39.9); H 3.4 (calcd. 3.4); N 12.6 (calcd. 12.7)%. ESI-
MS: m/z = 293.9939 (M+–Cl: 293.9944). X-ray: Single crystals of the
composition [Ni(7)Cl2(DMSO)]·DMSO (9a) were obtained by crys-
tallizing the compounds from DMSO in an atmosphere of MeOH.
H, H6*), 7.55 (dd, 1 H, H4*); 7.33 (ddd, 1 H, H5**); 7.11 (m, 3 H,
H5*, H4*, H3**); 6.31 (pt, 1 H, H1Ј); 6.22 (ddd, 1 H, H3*); 5.25 (s,
1 H, OH); 4.41 (m, 1 H, OH); 4.34 (dt, 1 H, H3Ј); 4.34 (dd, 1 H, H4Ј);
3.69–3.60 (m, 2 H, H5Ј, H5ЈЈ); 2.74 (dd, 1 H, H2Ј); 2.53 (dd, 1 H,
H2ЈЈ); 2.30 (s, 3 H, CH3). 13C NMR ([D4]Methanol): δ = 155.8 (C3);
150.3 (C2*); 150.0 (C6*); 146.7 (C2**); 134.6 (C4*); 131.8 (C4**);
126.9 (C5**); 125.4 (C3**); 124.1 (C5*); 113.1 (C3*); 88.6 (C4Ј);
86.4 (C1Ј); 71.1 (C3Ј); 62.4 (C5Ј); 40.8 (C2Ј); 14.1 (CH3).
C16H19N3O3S · 0.25H2O: C 56.9 (calcd. 56.9); H 5.7 (calcd. 5.8); N
12.3 (calcd. 12.4)%. ESI-MS: m/z = 356.1040 (M+Na+: 356.1045).
Synthesis of the Model Nucleobase (7): To a solution of 2b (0.99 g,
Synthesis of [Co(7)(NO3)2(H2O)] (10): The N,N,O-ligand 7 (81.3 mg,
8.11 mmol) in EtOH (30 mL), acetic acid (0.8 mL) and 2-furancarbox-
404 μmol) was dissolved in MeOH (10 mL). A solution of
aldehyde (0.67 mL, 0.79 g, 8.22 mmol) were added. The reaction mix- Co(NO3)2·6H2O (118.1 mg, 406 μmol) in MeOH (5 mL) was added.
ture was stirred at 55 °C for 35 min. The solvent was evaporated; the
residue was dissolved in CH2Cl2 (80 mL) and washed with water. After
The reaction mixture was refluxed at 80 °C for 3 h. The solvent was
evaporated and the residue treated with Et2O. The solid was filtered
evaporation of the organic phase the product was obtained in 71% off and washed with Et2O. After drying at 40 °C, the product was
yield (1.16 g, 5.76 mmol). 1H NMR (CDCl3): δ = 8.21 (ddd, 1 H,
obtained in 64% yield (104.1 mg, 259 μmol). C11H13CoN5O8
H6*); 7.69 (dd, 1 H, H5**); 7.59 (dd, 1 H, H4*); 7.53 (s, 1 H, H3);
(402.0096): C 32.7 (calcd. 32.9); H 3.4 (calcd. 3.3); N 17.5 (calcd.
Table 3. Crystallographic data for compounds 8, 9a, and 10.
8
9a
10
Empirical formula
Formula weight
C11H11Cl2CuN3O
335.67
C15H23Cl2N3NiO3S2
487.09
C11H13CoN5O8
402.19
Crystal system
Space group
monoclinic
P121/n1
triclinic
P1
monoclinic
P121/n1
¯
a /Å
b /Å
c /Å
α /°
13.2532(3)
7.53314(13)
13.7017(3)
90
8.3419(3)
9.6094(2)
13.4147(3)
12.0436(2)
90
11.3177(5)
12.5230(5)
97.372(4)
β /°
105.060(2)
90
1320.97(4)
4
100.634(3)
110.800(4)
1061.82(7)
2
92.090(1)
90
1551.47(5)
4
γ /°
V /Å3
Z
ρcalcd. /g·cm–3
μ(Mo-Kα) /mm–1
Crystal size /mm
Temperature /K
θmin, θmax /°)
Dataset
1.688
2.054
1.523
1.381
1.722
1.161
0.25ϫ0.22ϫ0.05
183(2)
2.48, 32.75
–19:18, –11:11, –20:20
25088, 4511
3670
4511, 175
0.0357, 0.0807, 1.075
0.48, –0.40
0.64ϫ0.53ϫ0.44
183(2)
2.81, 31.51
–12:12, –17:16, –17:17
18420, 6734
5331
6734, 244
0.0360, 0.0934, 1.003
0.70, –0.64
0.35ϫ0.28ϫ0.04
153(2)
2.27, 30.06
–13:13, –18:18, –16:16
23682, 4548
4025
4548, 233
0.0274, 0.0764, 1.044
0.75, –0.28
Tot., uniq. data
Observed data [I Ͼ 2σ(I)]
Nref, Npar
R, wR2, S [I Ͼ 2σ(I)]a)
Resd. dens. min. and max. /e·Å–3
2
2 2
2 2 1/2
a) R1 = Σ||Fo|–|Fc||/Σ||Fo|, wR2 = [Σw(Fo –Fc ) /Σw(Fo ) ]
.
1626 www.zaac.wiley-vch.de
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Z. Anorg. Allg. Chem. 2013, 1621–1627

A Family of Hydrazone-Based Nucleosides
17.7)%. ESI-MS: m/z = 340.0212 (M+–(NO3): 340.0218). X-ray: Sin-
gle crystals of 10 were obtained by crystallizing the product from
MeOH in an atmosphere of Et2O.
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Angew. Chem. Int. Ed. 2007, 46, 5602–5604.
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F. M. Bickelhaupt, J. Müller, Chem. Eur. J. 2011, 17, 6533–6544.
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ence 2003, 299, 1212–1213.
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Shionoya, T. Carell, Nat. Nanotechnol. 2006, 1, 190–194.
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X-ray Crystallography: Crystal data were collected with graphite-
monochromated Mo-Kα radiation (λ = 0.71073 Å) with an Xcalibur
system (8, 9a) and a Bruker APEX diffractometer (10). The structures
were solved by direct methods and were refined by full-matrix, least-
squares on F2 by using the SHELXTL PLUS and SHELXL-97 pro-
grams.[26] All non-hydrogen atoms were refined anisotropically, whilst
hydrogen atoms were calculated on ideal positions. In compound 8,
the equatorial chlorido ligand was found to be disordered over two
positions with occupancy factors of 0.60 and 0.40. Relevant crystallo-
graphic data are listed in Table 3.
Crystallographic data (excluding structure factors) for the structures in
this paper have been deposited with the Cambridge Crystallographic
Data Centre, CCDC, 12 Union Road, Cambridge CB21EZ, UK. [16] Y. Takezawa, K. Tanaka, M. Yori, S. Tashiro, M. Shiro, M.
Shionoya, J. Org. Chem. 2008, 73, 6092–6098.
[17] I. Okamoto, T. Ono, R. Sameshima, A. Ono, Chem. Commun.
2012, 48, 4347–4349.
Copies of the data can be obtained free of charge on quoting the de-
pository numbers CCDC-922129, CCDC-922130, and CCDC-922131.
(Fax: +44-1223-336-033; E-Mail: deposit@ccdc.cam.ac.uk, http://
www.ccdc.cam.ac.uk)
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Chem. 2001, 113, 3397–3399; Angew. Chem. Int. Ed. 2001, 40,
3397–3399; b) J. Müller, F.-A. Polonius, M. Roitzsch, Inorg.
Chim. Acta 2005, 358, 1225–1230; c) J. Müller, E. Freisinger, P.
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255–263; d) D. A. Megger, J. Kösters, A. Hepp, J. Müller, Eur.
J. Inorg. Chem. 2010, 4859–4864; e) K. Seubert, D. Böhme, J.
Kösters, W.-Z. Shen, E. Freisinger, J. Müller, Z. Anorg. Allg.
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T. Akitsu, Y. Aritake, Dalton Trans. 2011, 40, 3219–3228.
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Acknowledgements
Financial support by the Deutsche Forschungsgemeinschaft (IRTG
1143) is gratefully acknowledged. This work was performed within
the framework of COST Action CM1105 (EF, JM). We thank James
Reilly for performing some of the syntheses.
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Received: January 31, 2013
Published Online: March 19, 2013
Z. Anorg. Allg. Chem. 2013, 1621–1627
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.zaac.wiley-vch.de
1627