Synthesis and structure of a nucleoside with π-conjugated nitroxide spin label forming a one-dimensional ferromagnetic chain

Article abstract of DOI:10.1021/ja060846o

Spin labeled 2′-deoxyuridine, in which a significant fraction of the spin density is delocalized from a nitroxide radical to the DNA base residue, was prepared as a crystalline solid, stable at ambient conditions. The crystal packing, which includes multi

Full text of DOI:10.1021/ja060846o

Published on Web 03/30/2006
Synthesis and Structure of a Nucleoside with π-Conjugated Nitroxide Spin
Label Forming a One-Dimensional Ferromagnetic Chain
Kausik Das,† Maren Pink,‡ Suchada Rajca,† and Andrzej Rajca*,†
Department of Chemistry, UniVersity of Nebraska, Lincoln, Nebraska 68588-0304, and
IUMSC, Department of Chemistry, Indiana UniVersity, Bloomington, Indiana 47405
Received February 4, 2006; E-mail: arajca1@unl.edu
Scheme 1. Synthesis of Nitroxide Radicals 1 and 2a
Spin labeling is a powerful technique used in the study of
biological molecules, including oligonucleotides.1,2 Recently, nu-
cleosides with nitroxide radicals directly attached to the nucleobases
have been reported, though efforts to isolate and adequately
characterize them were not successful.3 Synthesis of such nucleo-
sides, in which spin density is delocalized into the nucleobase, could
lead to new probes for structure and dynamics of oligonucleotides.
Furthermore, hydrogen bonding driven crystal packing of nucleo-
sides may provide a new approach to control of crystal packing of
nitroxide radicals and thus to control of exchange coupling,
especially to attain ferromagnetic exchange coupling, in the solid
state.4,5
a (i) t-BuLi (2.5 equiv), THF, -78 °C, 2 h, ZnCl2 (12 equiv), rt; (ii)
Pd(OAc)2 (0.3 equiv), P(t-Bu)3 (0.6 equiv), 4 (0.6 equiv), -40 °C, 5 h;
Herein we describe the synthesis, isolation, and characterization
of spin labeled nucleosides 1 and 2, including the structure and
(iii) KOH (5.0 equiv), MeOH, THF, rt, 3 h; (iv) HF (2.5 M in THF/H2O,
3.0 equiv), rt, 1.5 h; (v) Ag2O (1.0 equiv based on 6), acetone, 0 °C, 3 h;
magnetism of crystalline 1. In 1 and 2, nitroxide radicals are
connected with 2′-deoxyuridine moieties via a π-conjugated p-
phenylene linker, providing stability at ambient conditions and
significant delocalization of spin density into the uracyl moiety.
The synthetic route to 1 and 2 is based upon Negishi cross-
coupling between the TBDMS-protected hydroxylamine 3 and
tritoluyl-protected 5-iodo-2′-deoxyuridine 4,6 to provide 5. Sequen-
tial deprotection of 5, followed by oxidation of hydroxylamine 7,
gives nitroxide radical 1. Analogous transformations provide
nitroxide radical 2 (Scheme 1).
(vi) HF (5.0 M in THF/H2O, 13.0 equiv), THF, rt, 1.5 h; (vii) Ag2O (7.0
equiv), CHCl3, rt, 2.5 h.
Both 1 and 2 are stable at ambient conditions, especially in the
solid state, and are purified by normal phase (and reversed phase
for 1) chromatography. The content of diamagnetic impurities is
negligible, as determined by both magnetic measurements and H
NMR spectroscopy (Figures S17, S22).
The structure of spin labeled nucleoside 1 was confirmed by
X-ray crystallography (Figure 1A). The π-systems of nitroxide,
p-phenylene, and uracyl are nearly coplanar, facilitating delocal-
ization of spin density into the base.7
1H NMR spectra of 6 mM 1 in acetone-d6 and 10 mM 2 in
chloroform-d do not show resonances for either the p-phenylene
linker or, notably, vinylic hydrogen at C6 (Figure 1A) of the uracyl
moiety, as expected for nuclei with significant spin density. In the
spectrum of 1, the most broadened and most shifted singlet at δ ≈
-5 ppm (∼9 H) is assigned to the hydrogens of the tert-butyl group.
Figure 1. (A) Molecular structure and conformation of nucleoside 1.
Carbon, oxygen, and nitrogen atoms are depicted with thermal ellipsoids
set at the 50% probability level. (B) Three unit cells showing molecular
packing of 1 into chains along the crystallographic a-axis (drawn using
Schakal).12 Intercepted lines correspond to the selected short intermolecular
distances shown in magenta (O14-C12) and turquoise (O2-C11).
1
EPR spectra of 3 mM 1 in acetone and 3 mM 2 in chloroform
show the expected coupling pattern for a 4-substituted phenyl-
nitroxide radical and an additional doublet splitting, aH ≈ 0.045-
0.046 mT, which is assigned to the vinylic hydrogen at C6 of the
1
uracyl moiety (Figure 1A and 2); the H-hyperfine splitting from
the hydrogens of the tert-butyl group is too small to be resolved.
Thus, both 1H NMR and EPR spectra indicate significant spin
delocalization into the uracyl moiety in 1 and 2.8
Magnetic studies for ∼0.007 M 1 in methanol and ∼0.07 M 2
† University of Nebraska.
‡ Indiana University.
in chloroform reveal the expected spin-1/2 paramagnetic behavior
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J. AM. CHEM. SOC. 2006, 128, 5334-5335
10.1021/ja060846o CCC: $33.50 © 2006 American Chemical Society

C O M M U N I C A T I O N S
both heavy atoms possess relatively large spin densities, may be
relevant to the observed exchange coupling in the solid state. The
closest intrachain contact between the neighboring molecules, O14-
C12 of 3.37 Å, may be viewed approximately as a π-π overlap
between the positive spin density of the nitroxide and negative spin
density at the meta-position of the benzene ring. Based upon the
McConnell model, such interaction should be ferromagnetic.14 Short
interchain contacts, such as O2-C11 of 3.16 Å along the b-axis,
are also found (Figure 1B); however, the O2 of the uracyl moiety
is expected to possess a rather small spin density.8 These two
contacts may be responsible for the stronger intrachain ferromag-
netic coupling and the weaker interchain antiferromagnetic coupling,
as observed in the solid-state magnetic data of 1.
In summary, spin labeled 2′-deoxyuridine, in which a significant
fraction of the spin density is delocalized from a nitroxide radical
to the DNA base residue, was prepared as a crystalline solid, stable
at ambient conditions. The crystal packing of 1, which includes
multiple hydrogen bonds, leads to one-dimensional chains of
molecules with predominant intrachain ferromagnetic coupling and
weaker interchain antiferromagnetic coupling.
Figure 2. EPR spectra of 3 mM 1 in acetone and 3 mM 2 in chloroform.
Black and red traces correspond to the experimental and simulated spectra,
respectively. The horizontal axes of the spectra are offset, due to different
microwave frequencies. Parameters for the simulations are shown in Figure
S2 (Supporting Information).
Acknowledgment. This research was supported by the National
Science Foundation (CHE-0414936, DMR-0216788, CHE-0107241).
Supporting Information Available: Experimental section, X-ray
crystallographic files in CIF format, and complete ref 8b. This material
is available free of charge via the Internet at http://pubs.acs.org.
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Figure 3. Main and left inset plots: øT vs T and numerical fit to eq 1.
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3
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respectively.
(8) (a) Using a model compound 9 (Figures S6-S9, Supporting Information),
in which the deoxyribose moiety is replaced with a methyl group, spin
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room temperature to øT ≈ 0.6 emu K mol-1 at 3 K; below 3 K,
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M/Msat vs H/T plots at 5, 3, and 1.8 K are bracketed by Brillouin
curves with S ) 1 and S ) 3/2, suggesting the presence of
intermolecular ferromagnetic exchange coupling between more than
two molecules of 1. The øT vs T data provide an excellent fit
(R2 ) 0.998) to a model for a 1-D spin-1/2 Heisenberg chain with
the following parameters: intrachain ferromagnetic coupling, J1/k
) 4.2 K, mean-field correction for an interchain antiferromagnetic
coupling, zJ2/k ) -1.2 K, and weight factor, w ) 1.07 (eq 1, Figure
3).10,11 Analogous three-parameter fits to alternative models, such
as a spin-1/2 pair (eq S2, Supporting Information), are decisively
inferior (R2 ) 0.96). Further support for a 1-D ferromagnetic chain
is provided by the crystal structure of 1.
(9) For relatively well-soluble 2, nearly quantitative values of magnetization
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(11) Equation 1: øT ) 0.5wø1DT/[1 - (2zJ2/3k)ø1D]ø1D ) (3/4kT)[(1 + a1 ‚ K
+ a2 ‚ K2 + a3 ‚ K3 + a4 ‚ K4 + a5 ‚ K5)/(1 + b1 ‚ K + b2 ‚ K2 + b3
‚
K3 + b4 ‚ K4)]2/3; a1 ) 5.797 991 6, a2 ) 16.902 653, a3 ) 29.376 885,
a4 ) 29.832 959, a5 ) 14.036 918, b1 ) 2.797 991 6, b2 ) 7.008 678 0,
b3 ) 8.653 864 4, b4 ) 4.574 311 4, K ) J1/2kT.
Molecules of 1 pack into one-dimensional chains extending along
the a-axis (Figure 1B). Both intrachain (O5′-H- - -O3′) and
interchain (N3-H- - -O5′, O3′-H- - -O14) classical hydrogen bonds
are found (Figure S1, Supporting Information) similar to those in
5-hydroxymethyl-2′-deoxyuridine.13 While such hydrogen bonds are
important for the crystal structure of 1, other short contacts, in which
(12) Keller, E. Schakal99, a computer program for graphic representation of
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