Metalated nucleobase quartets: Dimerization of a metal-modified guanine, cytosine pair of trans-(NH3)2Pt(II) and formation of CH···N hydrogen bonds

Article abstract of DOI:10.1021/ja981637+

The X-ray crystal structures of two complexes of the composition trans- [Pt(NH₃)₂(9-EtG-N7)(1-MeC-N3')]X·nH₂O (1) with 9-EtG = 9-ethylguaninate and 1-MeC = 1-methylcytosine are reported. 1b (X = picrate, n = 1) crystallizes to produce a dimetalated base quartet, held together by H- bonding interactions between pairs of cations. This feature essentially corresponds to the solution structure previously proposed by us on the basis of ¹H NMR and ESI-MS, with a H-bonding interaction between the aromatic H5' proton of 1-MeC and the deprotonated N1 position of 9-EtG. 1c (X = trifluoromethanesulfonate, n = 0) crystallizes in a radically different fashion as a consequence of nucleobase rotation about the Pt-N bond, leading to a reversed Hoogsteen arrangement without any intracomplex H bonding between the two bases. In the solid-state structure of 1b short intermolecular H bonds exist between the exocyclic NH₂ group of 1-MeC and O6 of 9-EtG (2.715(7) A?). Considerably longer intra- (N4'(1-Mec)···O6(9- EtG), 3.229(6) A?) and intermolecular (C5'(1-MeC)···N1(9-EtG), 3.548(7) A?) H bonds are primarily a consequence of considerable base twisting, presumably caused by stacking between the guanine residues and the picrate anions. In DMSO-d₆ solution, the cyclic base quartet structure is favored, regardless of the nature of the anion X (X = picrate, trifluoromethanesulfonate, perchlorate, nitrate). An association constant K(D) = 44.1 ± 3.2 M^-1 for the dimerization has been determined.

Full text of DOI:10.1021/ja981637+

12000
J. Am. Chem. Soc. 1998, 120, 12000-12007
Metalated Nucleobase Quartets: Dimerization of a Metal-Modified
Guanine, Cytosine Pair of trans-(NH3)2PtII and Formation of CH‚‚‚N
Hydrogen Bonds
Roland K. O. Sigel, Eva Freisinger, Susanne Metzger, and Bernhard Lippert*
Contribution from the Fachbereich Chemie, UniVersita¨t Dortmund, D-44221 Dortmund, Germany
ReceiVed May 11, 1998
Abstract: The X-ray crystal structures of two complexes of the composition trans-[Pt(NH3)2(9-EtG-N7)(1-
MeC-N3′)]X‚nH2O (1) with 9-EtG ) 9-ethylguaninate and 1-MeC ) 1-methylcytosine are reported. 1b (X
) picrate, n ) 1) crystallizes to produce a dimetalated base quartet, held together by H-bonding interactions
between pairs of cations. This feature essentially corresponds to the solution structure previously proposed
by us on the basis of 1H NMR and ESI-MS, with a H-bonding interaction between the aromatic H5′ proton of
1-MeC and the deprotonated N1 position of 9-EtG. 1c (X ) trifluoromethanesulfonate, n ) 0) crystallizes in
a radically different fashion as a consequence of nucleobase rotation about the Pt-N bond, leading to a reversed
Hoogsteen arrangement without any intracomplex H bonding between the two bases. In the solid-state structure
of 1b short intermolecular H bonds exist between the exocyclic NH2 group of 1-MeC and O6 of 9-EtG (2.715(7)
Å). Considerably longer intra- (N4′(1-MeC)‚‚‚O6(9-EtG), 3.229(6) Å) and intermolecular (C5′(1-MeC)‚‚‚
N1(9-EtG), 3.548(7) Å) H bonds are primarily a consequence of considerable base twisting, presumably caused
by stacking between the guanine residues and the picrate anions. In DMSO-d6 solution, the cyclic base quartet
structure is favored, regardless of the nature of the anion X (X ) picrate, trifluoromethanesulfonate, perchlorate,
nitrate). An association constant KD ) 44.1 ( 3.2 M-1 for the dimerization has been determined.
Introduction
obtained in DMSO-d6 solution and ESI mass spectrometry of a
MeOH solution.6,9 The most intriguing feature of the metalated
cyclic base quartet was the existence of two H bonds between
the aromatic H5′ proton of 1-MeC and the deprotonated ring
nitrogen atom N1 of 9-EtG each. To the best of our knowledge,
this had been the first report of this type of H bonding between
two nucleobases. Attempts to grow single crystals of 1a suitable
for X-ray crystallography had been unsuccessful for a long time.
We finally were able to obtain crystals of the picrate (1b), the
trifluoromethanesulfonate (1c), and the nitrate salt (1d). Even-
tually, only 1b and 1c permitted full structure determinations.
Substitution of a proton involved in H bonding between two
nucleobases by a metal entity of suitable geometry generates
complexes that are to be considered “metal-modified base
pairs”.1,2 These pairs can be converted into base triplets, either
by H bonding to a third base3 or by additional “metal-
modification”4 (Chart 1, i and ii). As we have recently found,
“metal-modified base pairs“ can also self-associate via H bond
formation to give open5 or cyclic6 base quartets (Chart 1, iii
and iv). The latter situation is of particular interest since it
relates to nucleobase quartets and tetrastranded nucleic acid
structures.7 The role of metal ions in stabilizing tetrastranded
DNA7 or RNA7 is to bind to carbonyl oxygen atoms of four or
eight bases, as also seen in model systems,8 rather than to cross-
link bases as in the present case. There is reason to believe
that even more ways to stabilize nucleobase quartets are
possible, e.g. by ammine ligands bound to a metal.8
Experimental Section
Preparations. 9-Ethylguanine (9-EtGH) was purchased from
Chemogen, Konstanz (Germany) and 1-methylcytosine was prepared
(7) Morgan, A. R. Nature 1970, 227, 1310-1313. (b) McGavin, S. J.
Mol. Biol. 1971, 55, 293-298. (c) Chernyi, A. A.; Lysov, Yu. P.; Il’ychova,
I. A.; Zibrov, A. S.; Shchyolkina, A. K.; Borisova, O. F.; Mamayeva, O.
K.; Florentiev, V. L. J. Biomol. Struct. Dynam. 1990, 8, 513-527. (d)
Borisova, O. F.; Golova, Yu. P.; Gottikh, B. P.; Zibrov, A. S.; Il’ychova,
I. A.; Lysov, Yu. P.; Mamayeva, O. K.; Chernov, B. K.; Chernyi, A. A.;
Shchyolkina, A. K.; Florentiev, V. L. J. Biomol. Struct. Dynam. 1991, 9,
1187-1210. (e) Gaillard, C.; Strauss, F. Science 1994, 264, 433-436. (f)
Lebrun, A.; Lavery, R. J. Biomol. Struct. Dynam. 1995, 13, 459-646 and
references cited. (g) Kang, C.; Zhang, X.; Moyzis, R.; Rich, A. Nature
1992, 356, 126-131. (h) Laughlan, G.; Murchie, A. I. H.; Norman, D. G.;
Moore, M. P.; Moody, P. C. E.; Lilley, D. M. J.; Luisi, B. Science 1994,
265, 520-524. (i) Sarma, M. H.; Luo, J.; Umemoto, K.; Yuan, R.-da.;
Sarma, R. H. J. Biomol. Struct. Dynam. 1992, 10, 1131-1142. (j) Cheong,
C.; Moore, P. B. Biochemistry 1992, 31, 8406-8414.
(8) Witkowski, H.; Freisinger, E.; Lippert, B. J. Chem. Soc., Chem.
Commun. 1997, 1315-1316.
(9) Abbreviations used: 9-MeA ) 9-methyladenine; 9-EtGH ) 9-eth-
ylguanine; 9-EtG ) 9-ethylguaninate anion (deprotonated at N1); 7,9-DimeG
) 7,9-dimethylguanine; 1-MeC ) 1-methylcytosine; 1-MeU ) 1-methyl-
uracil anion; Pt donor sites are indicated by N7, N3, etc.; ESI-MS )
electrospray ionization mass spectrometry.
Situation (iv) had been encountered by us for trans-[Pt(NH3)2(9-
EtG-N7)(1-MeC-N3′)]ClO4 (1a) according to H NMR data
1
(1) Krizanovic, O.; Sabat, M.; Beyerle-Pfnu¨r, R.; Lippert, B. J. Am. Chem.
Soc. 1993, 115, 5538-5548 and references cited.
(2) For other examples of H bonds replaced by metal ions of linear
geometry, see, e.g.: (a) HgII: Yamane, T.; Davidson, N. J. Am. Chem.
Soc. 1961, 83, 2599-2607. (b) CuII: Sundaralingam, M.; Carrabine, J. A.
J. Mol. Biol. 1971, 61, 287-309. (c) AgI: Shin, Y. A.; Eichhorn, G. L.
Biopolymers 1980, 19, 539-556 and references cited.
(3) Dieter-Wurm, I.; Sabat, M.; Lippert, B. J. Am. Chem. Soc. 1992,
114, 357-358.
(4) Schreiber, A.; Lu¨th, M. S.; Erxleben, A.; Fusch, E. C.; Lippert, B. J.
Am. Chem. Soc. 1996, 118, 4124-4132. (b) Lu¨th, M. S.; Freisinger, E.;
Glahe´, F.; Mu¨ller, J.; Lippert, B. Inorg. Chem. 1998, 37, 3195-3203.
(5) Metzger, S.; Britten, J. F.; Erxleben, A.; Lock, C. J. L.; Albinati, A.;
Lippert, B. Submitted for publication. (b) Meiser, C.; Freisinger, E.; Lippert,
B. J. Chem. Soc., Dalton Trans. 1998, 2059-2064.
(6) Metzger, S.; Lippert, B. J. Am. Chem. Soc. 1996, 118, 12467-12468.
10.1021/ja981637+ CCC: $15.00 © 1998 American Chemical Society
Published on Web 11/06/1998

Metalated Nucleobase Quartets
J. Am. Chem. Soc., Vol. 120, No. 46, 1998 12001
1106 Strumentazione Element-Analyzer. The stability constant was
calculated on an IBM-compatible PC with a curve fitting procedure
that used a nonlinear Newton-Gauss least-squares program (see also
below).
Chart 1
Determination of the Association Constant. The experimental
conditions of the dilution experiment were the same as described in
ref 6. At different concentrations of 1a in DMSO-d6, the chemical
shifts of H5′, H6′, and the two hydrogen atoms at N4′ of 1-MeC were
evaluated for the calculation of the stability constant for the dimerization
by application of eq 1, which provides the relationship for the observed
1 - (8KD[A] + 1)1/2
δobs ) δD + (δD - δo)
(1)
4KD[A]
chemical shift (δobs) and the various concentrations of the cation 1[A].
Equation 1 was derived in analogy to ref 12 where the self-association
of nucleosides and nucleotides was investigated. δo represents the
chemical shift of the protons at infinite dilution (i.e., when only
monomers are present in solution), δD represents the shift of the dimer,
and KD is the association constant as defined in eqs 2a and 2b.
A + A h A2
(2a)
(2b)
KD ) [A2]/[A]2
The unknown parameters were determined by starting an iterative
calculation with estimated values and varying them until the standard
deviation reaches a minimum (nonlinear Newton-Gauss least-squares
regression).
according to ref 10. trans-[(NH3)2PtCl2] was synthesized according
to the method of Kauffman and Cowan11 from K2PtCl4 (Degussa
(Germany)). The synthesis of trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-
N3′)]ClO4 (1a) from trans-[Pt(NH3)2(9-EtGH-N7)(1-MeC-N3′)](ClO4)25a
has been reported.6
Distance Calculation in Solution. The NOESY spectrum was taken
at a spectral width of 4802 Hz with a mixing time of 400 ms. The
sample concentration was 17 mM, corresponding to a dimerization
degree of 41.1 ( 2.1%. 256 FIDs of 1 K data points each were recorded
in a phase-sensitive mode using the TPPI method.13 Data were zero-
filled to a final size of 2 K × 1 K data points and multiplied by a 90°
shifted, squared sine bell window function prior to Fourier transforma-
tion. A fifth order polynomial baseline correction in both dimensions
was performed before integration. Integrals of cross-peaks between
N2H2/H5′, N2H2/H6′, and H5′/H6′, respectively, were computed by
adding all signal intensities within manually chosen integration regions
(uxnmr). Distances between the N2H2 protons of guanine and the H5′
and H6′ protons of cytosine were calculated with eq 314
trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-N3′)](C6H2N3O7)‚H2O (1b) was
prepared by combining aqueous solutions of trans-[Pt(NH3)2(9-EtGH-
N7)(1-MeC-N3′)](NO3)2 (15 mL, c ) 10 mM) and of picric acid (15
mL, c ) 10 mM), both brought to pH 10.7 (NaOH). The orange
precipitate that formed immediately was redissolved by stirring the
mixture at 80 °C under N2. The solution was slowly cooled to room
temperature and kept for several weeks under exclusion of air, before
the orange microcrystalline powder that had formed was filtered off,
washed with water, and dried at 40 °C. The yield of 1b was 82%.
Recrystallization from a dilute ethanolic solution and slow evaporation
of the alcohol gave larger crystals which were suitable for X-ray
analysis. Anal. Calcd (found) for C18H25N13O10Pt: C 27.77 (27.6); H
3.24 (3.3); N 23.39 (23.4).
trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-N3′)](CF3SO3) (1c). trans-
[Pt(NH3)2(9-EtGH-N7)(1-MeC-N3′)](ClO4)2 (217 mg, 0.3 mmol) was
dissolved in water (20 mL) and passed over an anion exchange column
that had been loaded with chloride. The eluate was evaporated to
dryness to give trans-[Pt(NH3)2(9-EtGH-N7)(1-MeC-N3′)]Cl2 (167 mg).
To an aqueous solution of trans-[Pt(NH3)2(9-EtGH-N7)(1-MeC-N3′)]Cl2
(8 mL, c ) 16.5 mM) was added AgCF3SO3 (0.95 equiv), and the
mixture was stirred in the dark at room temperature overnight. After
removal of AgCl, the solution was brought to pH 10.7 with 1 M NaOH
and then allowed to evaporate slowly at room temperature under N2.
A small amount of crystalline platelets of 1c suitable for X-ray analysis
was isolated.
1/6
xD
r1 ) rH5′-H6′
I
(3)
(
)
H5′-H6′
I
on the basis of a r6 dependency of the cross-peak integrals I, using the
H5′-H6′ distance of cytosine (rH5′-H6′ ) 2.4 Å) and the integral of the
cytosine H5′/H6′ cross-peak IH5′-H6′ as references and taking into
account that only dimers give rise to N2H2/H5′ and N2H2/H6′ cross-
peaks, while all molecules contribute to the H5′/H6′ cross-peak. xD
corresponds to the molar fraction of cations 1 forming dimers.
X-ray Structure Determination of 1b and 1c. All X-ray data were
collected on an Enraf-Nonius-KappaCCD diffractometer15 with graphite-
monochromated Mo KR radiation (λ ) 0.71069 Å). Preliminary
orientation matrixes and unit cell parameters were obtained from the
peaks of the first 10 frames, respectively, and refined by using the whole
data set of 360 frames. Frames were integrated and corrected for
Lorentz and polarization effects by using DENZO.16 The scaling as
well as the global refinement of crystal parameters was performed by
SCALEPACK.16 Reflections, which were partly measured on previous
and following frames, are used to scale these frames on each other.
trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-N3′)](NO3)‚xH2O (1d). trans-
[Pt(NH3)2(9-EtGH-N7)(1-MeC-N3′)](NO3)2‚H2O (26 mg, 39 µmol) was
dissolved in water (3 mL) and brought to pH 10.7 (NaOH). Slow
evaporation of the solution at room temperature under N2 gave a few
crystals of 1d of poor quality which allowed no full structure
determination.
Instrumentation. 1H NMR spectra were recorded at 20 °C on a
Bruker AC 200 FT NMR spectrometer with DMSO-d6 (with TMS as
internal standard) as solvent without suppression of solvent signals.
The NOESY spectrum was recorded on a Bruker DRX 400 spectrometer
at 400.13 MHz and processed with standard software (uxnmr by
Bruker). Elemental analysis was performed with a Carlo Erba Model
(12) (a) Mitchell, P. R.; Sigel, H. Eur. J. Biochem. 1978, 88, 149-154.
(b) Scheller, K. H.; Hofstetter, F.; Mitchell, P. R.; Prijs, B.; Sigel, H. J.
Am. Chem. Soc. 1981, 103, 247-260.
(13) Marion, D.; Wu¨thrich, K. Biochem. Biophys. Res. Commun. 1983,
113, 967-974.
(14) Goljer, I.; Bolton, P. H. Two-Dimensional NMR-Spectroscopy.
Applications for Chemists and Biochemists, 2nd ed.; Croasmun, J. K.,
Carlson, R. M. K., Eds.; VCH: Weinheim, 1994; pp 699-740.
(15) NONIUS BV, KappaCCD package, Ro¨ntgenweg 1, P. O. Box 811,
2600 AV Delft, The Netherlands.
(10) Kistenmacher, T. J.; Rossi, M.; Caradonna, J. P.; Marzilli, L. G.
AdV. Mol. Relax. Interact. Proc. 1979, 15, 119-133.
(11) Kauffman, G. B.; Cowan, D. O. Inorg. Synth. 1963, 7, 239-245.

12002 J. Am. Chem. Soc., Vol. 120, No. 46, 1998
Sigel et al.
Table 1. Crystallographic Data for
trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-N3′)](C6H2N3O7)‚H2O (1b) and
trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-N3′)](CF3SO3) (1c)
1b
1c
formula
C18H25N13O10Pt
778.60
C13H21N10O5SF3Pt
681.55
fw (g mol-1
)
crystal system
space group
crystal color
crystal habit
a (Å)
b (Å)
c (Å)
triclinic
P1h (No. 2)
red
monoclinic
P2h1 (No. 4)
colourless
columns
10.562(2)
7.291(1)
block
8.884(2)
10.670(2)
15.620(3)
74.23(3)
76.75(3)
67.19(3)
1300.6(5)
2
15.259(3)
R (deg)
â (deg)
106.81(3)
γ (deg)
V (Å3)
1124.8(3)
2
31561/2574/266
0.0380
0.0792
1.086
Z
data/obsda/params.
R1(obsd data)b
wR2(obsd data)c
GOFd
34933/3399/396
0.0301
0.0595
1.016
a Observation criterion I > 2σ(I). b R1 ) ∑||Fo| - |Fc||/∑|Fo|. c wR2
2
) [∑w(Fo2 - Fc2)2/∑w(Fo )2]1/2
.
d GOF ) [∑w(Fo2 - Fc2)2/(n - p)]1/2
,
with n ) number of reflections and p ) number of parameters.
This procedure in part eliminates absorption effects and also considers
a crystal decay if present.
All structures were solved by standard Patterson methods17 and
refined by full-matrix least-squares based on F2, using the SHELXTL
PLUS18 and SHELXL-93 programs.19
1b: Data collection was performed with a collecting time of 50 s
per frame. The non-hydrogen atoms were refined anisotropically.
Hydrogen atoms were placed in geometrical calculated positions except
for the aromatic hydrogens of the nucleobases, which were found with
difference Fourier syntheses, and refined with a common isotropic
temperature factor.
Figure 1. Concentration dependency of the chemical shifts of 1 in
DMSO-d6 in the concentration range 0-85 mM. The data from top to
bottom correspond to N4′H2 (1) and N4′H1 (2) of 1-MeC, H8 (+) of
9-EtG, H6′ (9) and H5′ (b) of 1-MeC, and N2H2 ([) of 9-EtG.
1c: The collection time of the intensity data was 60 s per frame.
The non-hydrogen atoms were refined anisotropically, except for the
disordered ethyl group, which was modeled with occupancies of 0.44
(C92A) and 0.56 (C92B), and the atoms of the anion except for sulfur.
Hydrogen atoms were included at calculated positions but not refined.
Crystal data and data collection parameters are summarized in
Table 1.
that as a consequence of guanine deprotonation in 1, actually a
slight upfield shift of the 1-MeC resonances as compared to
trans-[Pt(CH3NH2)2(1-MeC)2]2+ might have been expected. As
to the resonance of the amino group of 1-MeC, it is split in a
1:1 ratio at the lowest concentration applied and at concentra-
tions g10 mM (Figure 1). Splitting of this resonance is to be
attributed to either of the three following reasons or combina-
tions thereof: (i) binding of a Pt electrophile at N3′, which
increases the double bond character of the C4′-N4′ bond and
hence makes fast rotation of the amino group more difficult,
(ii) anion binding to the amino proton,21 or (iii) H bonding in
general. In the present case, it is to be considered a combination
of (i) and (iii). Clearly, the concentration dependency of one
of the two components reflects its involvement in intermolecular
association. The second component of the NH2 resonance,
downfield from the former only at very low concentrations but
otherwise little affected (9.1-9.2 ppm), has to be due to an
intramolecularly H bonded proton (viz. to O6 of 9-EtG, as seen
in the solid-state structure of 1b). Only if H bonded can the
relatively large downfield shift of this resonance be explained.22
For example, in cases with no intramolecular H bond formation
possible, such as in trans-[Pt(CH3NH2)2(1-MeC)Cl]Cl, the
amino protons of 1-MeC resonate at considerably higher field,
at 8.29 and 8.72 ppm.23 The NH2 resonance of 9-EtG is almost
concentration-independent and therefore practically does not
participate in the association process.
Results and Discussion
Solution Behavior. All four compounds 1a-1d behave
identically in DMSO-d6 solution as far as the concentration
dependency of the H5′ proton and of one of the 4′-amino protons
of the 1-MeC is concerned (Figure 1). This clearly indicates
that the monomer h dimer equilibrium postulated for 1a does
not depend on the anion. The concentration-independent shift
of the picrate proton resonance of 1b (8.59 ppm; 0.6-30.5 mM)
further confirms this conclusion. Comparison of the chemical
shifts (DMSO-d6) of H5′ and H6′ cytosine resonances of 1a-
1d with trans-[Pt(CH3NH2)2(1-MeC)2]2+ 20 reveals the follow-
ing: At concentrations where the H5′ chemical shift is more or
less constant (g0.1 M; δ(H5′) ≈ 7.2 ppm), this resonance is
downfield by 1.2 ppm in 1, whereas the H6′ resonances in the
compounds differ very slightly only. This is so despite the fact
(16) Otwinowsky, Z.; Minor, W. Processing of X-ray Diffraction Data
Collected in Oscillation Mode. In Methods in Enzymology; Carter, C. W.,
Sweet, R. M., Jr., Eds.; Academic Press: New York, 1996, p 276.
(17) Sheldrick, G. M. Acta Crystallogr. 1990, A46, 467.
(18) Sheldrick, G. M. SHELXTL PLUS (VMS), Siemens Analytical
X-ray Instruments, Inc.: Madison, WI, 1990.
(19) Sheldrick, G. M. SHELXL-93, Program for crystal structure
refinement, University of Go¨ttingen, Germany, 1993.
(20) Holthenrich, D.; So´va´go´, I.; Fusch, G.; Erxleben, A.; Fusch, E. C.;
Rombeck, I.; Lippert, B. Z. Naturforsch. 1995, 50b, 1767-1775.
(21) Rossi, M.; Caradonna, J. P.; Marzilli, L. G.; Kistenmacher, T. J.
AdV. Mol. Relax. Interact. Proc. 1979, 15, 103-117.
(22) Hegmanns, A.; Freisinger, E.; Zangrando, E.; Ashfar, A.; Hu¨bener,
E.; Appleton, T. G.; Lippert, B. Inorg. Chim. Acta 1998, 279, 152-158.
(23) Pesch, F. J.; Preut, H.; Lippert, B. Inorg. Chim. Acta 1990, 169,
195-200.

Metalated Nucleobase Quartets
J. Am. Chem. Soc., Vol. 120, No. 46, 1998 12003
Table 2. Individual Results Obtained from the Curve Fitting
Procedure Based on Eq 1 for the Dimerization of 1 in DMSO-d6
(20 °C)a
δ0 [ppm]
δ∞ [ppm]
KD* [M-1
]
KD [M-1
]
H5′
H6′
5.911 ( 0.012 7.213 ( 0.013 45.8 ( 4.5
7.799 ( 0.002 7.853 ( 0.002 45.3 ( 11.5
44.1 ( 3.2
}
N4′H2 8.695 ( 0.013 10.419 ( 0.018 41.7 ( 5.1
a δ0 corresponds to the calculated chemical shift of the monomer
whereas δ∞ is the calculated shift of the dimer species. Both protons
involved directly in dimerization (H5′ and N4′H2) as well as the
neighboring proton H6′ (all from the cytosine moiety) were evaluated
giving three individual results for the association constant KD*. The
final association constant KD (see eqs 2a and 2b) in the column to the
right corresponds to the weighted mean of the four results in the fourth
column with two times the error limit. All other error limits correspond
to one standard deviation.
Figure 2. Cation trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-N3′)]+, picrate
anion, and water molecule of compound 1b with atom numbering
scheme. Ellipsoids are at the 50% probability level.
Table 3. Selected Dihedral Angles (deg) and H-Bonding
Distances (Å) in the Crystal Structures of 1b and 1c
For determination of the association constant the data sets of
the 1-MeC resonances H5′, H6′, and N4′H2 (the proton of the
amino group of 1-MeC, which is directly involved in the
intermolecular H bond) were evaluated. The individual as-
sociation constants (KD*), which are given in Table 2, were
calculated by applying eq 1. The concentration range of the
cation 1 was between 0.47 and 72.2 mM for all three protons
used for evaluation because at larger concentrations only the
H5′ and H6′ resonances yet not the one from the amino proton
could be detected. The concentration dependency is much larger
with H5′ and the amino group than with H6′. However, this
finding is not surprising because the latter one itself is not
involved in hydrogen bonding. Still, the value obtained agrees
excellently with the values obtained for H5′ and the amino
proton. The final constant for the dimerization
1b
1c
174.2(4)
120(1)
6.0(4)
N7-Pt-N3′
C6-N1-C2
G/C
Pt-N7
Pt-N3′
N4′‚‚‚O6a
N4′‚‚‚O6
O2‚‚‚O6
C5′‚‚‚N1
N4′‚‚‚N1
N2‚‚‚N3a
N10‚‚‚O2′
N10‚‚‚O6
178.4(2)
120.0(5)
20.2(3)
2.008(4)
1.986(8)
2.022(8)
2.024(4)
2.715(7)
3.229(6)
4.35(1)
2.80(1)
3.548(7)
3.229(6)
2.91(3)/2.95(3)
2.92(3)/2.86(3)
angles of 1b are listed in Table 3 and compared with those of
the trifluoromethanesulfonate salt 1c. In 1b the two bases are
bound to Pt via the guanine N7 and cytosine N3′ positions and
adopt a Hoogsteen arrangement with the N3′ proton of cy-
tosinium replaced by the trans-(NH3)2PtII residue, very much
like the two bases of the parent compound trans-[(NH3)2Pt(9-
KD ) 44.1 ( 3.2 M-1
as it is defined by eqs 2a and 2b, corresponds to the weighted
mean of the three individual constants KD* obtained for H5′,
H6′, and N4′H2. The error given is two times the standard
deviation. It should be noted that all data sets could be fitted
with this final result by keeping KD constant and varying only
δ0 and δ∞, which correspond to the calculated chemical shifts
of the monomer or the dimer, respectively. The calculated
results for δ0 and δ∞, obtained with KD, are shown in Table
2.24
The other amino proton of 1-MeC which itself is involved
in the intramolecular H bond and also the data sets of H8 and
the amino group of 9-EtG could be fitted with this result as
well, even though the resonances are only slightly affected in
these cases by the dimerization.
EtGH)(1-MeC)]2+ 5a
As far as the overall geometry of the
.
complex is concerned, there are several differences between the
parent compound (isolated as two slightly different modifica-
tions) and 1b: Among these, the N7(guanine)-Pt-N3′(cytosine)
angle (178.4(2)° in 1b, but 175.0(2)° in one of the two
modifications of the parent complex5a) and the considerably
higher propeller twist between the two bases in 1b (20°) as
compared to the starting compound (5.5° and 6.3°) need to be
mentioned. Both features add up to a considerably longer
intramolecular O6‚‚‚N4′ separation in 1b (3.229(6) Å) as
compared to trans-[Pt(NH3)2(9-EtGH)(1-MeC)](ClO4)2‚nH2O
(3.00(2) and 3.11(1) Å)5a or related mixed purine-N7, pyrimi-
dine-N3′ nucleobase complexes of trans-(NH3)2PtII.1,3,5,27 We
are aware that the angles at the Pt coordination sites, e.g., Pt-
N7-C5, Pt-N7-C8 and Pt-N3′-C2′, Pt-N3′-C4′, likewise
have an influence on this intracomplex distance.5b,28 Another
difference refers to the intramolecular ring angle at N1 of
guanine, which is significantly smaller in 1b (120.0(5)°) as
compared to the starting compound (127.3(7)° and 128(1)°) or
neutral guanine in general,29,30 and reflects deprotonation of the
N1 position in 1b.31 It appears that the propeller twist of the
two bases in 1b is primarily caused by the picrate anion, which
The value KD ) 44.1 ( 3.2 M-1 obtained for the dimerization
of 1 compares with K ) 3.7 ( 0.6 M-1 for the Watson-Crick
pair between guanosine and cytidine at 32 °C in the same
solvent25 and with K ) 6.7 ( 0.2 M-1 (30 °C) for a 2:1 mixture
of DMSO and methanol.26 Provided compound 1 could be
derivatized to make it soluble in aprotic solvents, very high
association constants could indeed be expected.
X-ray Crystal Structure of 1b: A Diplatinated Nucleobase
Quartet. A view of the cation, anion, and water molecule of
trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-N3′)](C6H2N3O7)‚H2O (1b)
is depicted in Figure 2. Selected interatomic distances and
(27) Beyerle-Pfnu¨r, R.; Brown, B.; Faggiani, R.; Lippert. B.; Lock, C.
J. L. Inorg. Chem. 1985, 24, 4001-4009.
(28) Metzger, S.; Erxleben, A.; Lippert, B. J. Biol. Inorg. Chem. 1997,
2, 256-264.
(29) Taylor, R.; Kennard, O. J. Mol. Struct. 1982, 78, 1-28.
(30) Clowney, L.; Jain, S. C.; Srinivasan, A. R.; Westbrook, J.; Olson,
W. K.; Berman, M. J. J. Am. Chem. Soc. 1996, 118, 509-518.
(31) Singh, C. Acta Crystallogr. 1965, 19, 861-864.
(24) The previously6 obtained association constant (KD ) 59.1 ( 1.0
M-1) is sligthly higher than the one calculated now, but has been calculated
with a different method.
(25) Newmark, R. A.; Cantor, C. R. J. Am. Chem. Soc. 1968, 90, 5691-
5017.
(26) Peterson, S. B.; Led, J. J. J. Am. Chem. Soc. 1981, 103, 5308-
5313.

12004 J. Am. Chem. Soc., Vol. 120, No. 46, 1998
Sigel et al.
Figure 3. Association of quartets of 1b. Hydrogen atoms are not found in the Fourier-difference map; the water molecules as well as the picrate
anions are omitted for clarity.
stacks on top of the guanine base. The guanine moiety and the
aromatic ring of the picrate anion are nearly coplanar (deviation
2°) and 3.5 Å apart.
A view of the way cations of 1b are associated via H bonds
is given in Figure 3. Essentially the arrangement deduced by
1H NMR spectroscopy is verified. The two trans-[Pt(NH3)2(9-
EtG)(1-MeC)]+ cations are connected by two short intermo-
lecular H bonds between O6 sites of guanine and N4′ sites of
cytosine. The length, 2.715(7) Å, is definitely at the lower end
of H bonds typically found between nucleobases.32 On the other
hand the two separations between C5′ of the cytosine and N1
of guanine are rather long, 3.548(7) Å. Since the proton at C5′
was located in the difference Fourier synthesis, details of this
contact can be quantified: C5′-H5′, 0.88(5) Å, H5′-N1,
2.71(6) Å, and C5′-H5′-N1, 160(5)°. The H5′‚‚‚N1 separation
of 2.71(6) Å is slightly shorter than the sum of the van der
Waals radii of H (1.20 Å) and N (1.55 Å,33 1.60 Å34,35), but it
has to be taken into account that the radius for a negatively
charged N atom, as present here, is expected to be even larger.
Compared to typical CH‚‚‚N hydrogen bonds,35 which have
proton-nitrogen separations between 2.3 and 2.7 Å,33a,35 this
value should then still be considered a H bond. Again,
inspection of a model reveals that a reduction in nucleobase
propeller twist within the mononuclear entities brings about a
shortening of both the intramolecular O6-N4′ and the inter-
molecular C5′-N1 distance if the intermolecular O6-N4′
separation is kept constant. If a slight lengthening of the
intermolecular H bonds between O6 and N4′ is allowed, and
coplanarity of the four bases assumed, all six H bonds can be
within the usual 2.9-3.2 Å margin typically seen in nucleobase
associates. We therefore propose that the two “long“ distances
are essentially a consequence of the mentioned stacking effect
of the counterion.
Figure 4. Involvement of H8 proton of 9-EtG in 1b in H bonding
with a water molecule and an oxygen atom of the picrate anion,
respectively.
Chart 2
are 3.373(5) Å and 3.318(4) Å, clearly longer than the N4′‚‚‚O
separations (2.980(5), 2.992(4) Å) (Chart 2).
There are at least two additional interesting features of the
crystal packing. First, nucleobase quartets are linked by pairs
of weak H bonds of 3.229(6) Å between respective N2 and N3
sites of adjacent guanines, which are related by an inversion
center as shown in Figure 3. This pattern is similar to that seen
in the parent compound (2.95(1) Å)5a and in [9-EtGH2]2[PtCl4]
(3.05 Å)36 and it corresponds to that realized in homoguanine
pairs of parallel DNA.37 Second, the guanine H8 proton of the
It is to be noted that involvement of H5′ of cytosine in H
bonding has some precedence: Protonated cytosine model
nucleobases crystallize with ClO4- and NO3- anions in such a
way that H5′ and one of the two NH2 protons make H bonding
contacts to two oxygen atoms of the anion.21 C5′‚‚‚O contacts
(32) Saenger, W. Principles of Nucleic Acid Structure; Springer; New
York, 1984.
(33) (a) Taylor, R.; Kennard, O. J. Am. Chem. Soc. 1982, 104, 5063-
5070. (b) Bondi, A. J. Phys. Chem. 1964, 68, 441-451.
(34) Nyburg, S. C.; Fearman, C. H. Acta Crystallogr. 1985, B41, 274-
279.
(36) (a) Purnell, L. G.; Hodgson, D. J. J. Am. Chem. Soc. 1976, 98,
4795-4763. (b) Voet, D.; Rich, A. Prog. Nucleic Acid Res. Mol. Biol. 1970,
10, 183-265 and references cited.
(37) Robinson, H.; van der Marel, G. A.; van Boom, J. H.; Wang, A. H.
J. Biochemistry 1992, 31, 10510-10517.
(35) Mascal, M. J. Chem. Soc., Chem. Commun. 1998, 303-304.

Metalated Nucleobase Quartets
J. Am. Chem. Soc., Vol. 120, No. 46, 1998 12005
Figure 5. Aromatic part of the NOESY spectrum of 1 in DMSO-d6 solution (left) with crosspeaks due to through-space coupling between H5′ of
1-MeC and NH2 of 9-EtG indicated by broken lines, and scheme of relevant NOE contacts (right).
9-EtG ligand is involved in a bifurcated H bond with oxygen
atoms of a water molecule (3.274(9) Å) and of a picrate anion
(3.272(8) Å) (Figure 4). The two angles C8-H8-O are 142(5)°
and 130(5)° and the O-H8-O angle is 87(2)°. Similar contacts
between aromatic nucleobase protons and oxygen acceptor
atoms have been experimentally verified in a number of
cases21,38 and are presently subject to speculations concerning
their possible role in nucleic acid recognition.39
Nucleobase Quartet Structure: Comparison of Solid State
and Solution Structure. The NOESY cross-peak observed
between cytosine-H5′ and guanine-N2H2 in DMSO-d6 solution
was clearly supportive of the postulated quartet structure.
Calculation of the intramolecular distances in solution with the
aid of eq 3 gave 2.8 Å for the N2H2-H5′ and 3.5 Å for the
N2H2-H6′ distance, respectively. These two values compare
with the situation in the solid state where distances of 3.24(6)
(N2H2-H5′) and 3.94(5) Å (N2H2-H6′) are found. This
difference is readily rationalized if one assumes that the propeller
twist of the nucleobases in the crystal structure of 1b is lost in
solution, leading to coplanarity of the four nucleobases.
Figure 6. Cation of trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-N3′)](CF3SO3)
(1c) with atom numbering scheme. Ellipsoids are at the 50% probability
level.
our calculations, we have neglected the contribution of the
second amino proton pointing away from the cytosine ring. This
proton is about 1.7 Å further apart from the aromatic cytosine
protons than the amino proton (pointing toward the cytosine
ring). Therefore, we have estimated the contribution of the
second proton to the cross-peak integral to be less than 6%.
It should be noted that the resulting distances between N2H2
and H5′/H6′ in solution are only rough estimates for the
following reasons. First, as the molecule is very small, a mixing
time as high as 400 ms had to be chosen. Therefore, spin
diffusion and relaxation may affect cross-peak intensities.
Second, at the high sample concentration chosen for our
measurements (to achieve a satisfying degree of dimerization),
nonspecific intermolecular interactions may contribute to the
investigated cross-peaks.40 Nevertheless, no unexpected cross-
peaks indicative of nonspecific interactions have been detected
in the spectrum. Third, it has to be mentioned that the N2H2
resonance of guanine is an average signal of two amino protons
having different distances to the aromatic cytosine protons. In
X-ray Crystal Structure of 1c: A Metalated Base Pair
(only). The solid-state structure of trans-[Pt(NH3)2(9-EtG-
N7)(1-MeC-N3′)](CF3SO3) (1c) is radically different from that
of 1b in that the two bases adopt a reversed Hoogsteen
arrangement with the exocyclic oxygen atoms of the two bases
facing each other (Figure 6). Selected interatomic distances
and angles of 1c are included in Table 3. As can be seen, the
separation between guaninate-O6 and cytosine-O2′ is large
(4.35(1) Å) and in agreement with the deviation from linearity
of the Pt-N(nucleobase) vectors (N3′-Pt-N7, 174.2(4)°). The
orientation of the two nucleobases contrasts that of all presently
known metal complexes containing mixed pyrimidine-N3′,
purine-N7 combinations (cytosine/guanine,5a cytosine/adenine,27
thymine/adenine1) of linearly coordinated metal ions, since it
avoids intracomplex H bonding between the 6-position of the
purine and the 4′- or 2′-positions of the pyrimidine base. As a
consequence of this orientation in 1c a cyclic quartet structure
is excluded. Differences in cation-anion contacts are probably
responsible for this fact. The resulting cation-cation interac-
tions of 1c are depicted in Figure 7: There are two motifs
recognized. First, pairs of cations stack (ca. 3.4 Å) and form
pairs of H bonds between the NH3 groups and O6 of the 9-EtG
(38) See, e.g.: (a) Wahl, M. C.; Rao, S. T.; Sundaralingam, M. Nature
Struct. Biol. 1996, 3, 24-31. (b) Wahl, M. C.; Sundaralingam, M. TIBS
1997, 22, 98-102. (c) Leonard, G. A.; McAuley-Hecht, K.; Brown, T.;
Hunter, W. N. Acta Crystallogr. 1995, D51, 136-139. (d) Beyerle-Pfnu¨r,
R.; Jaworski, S.; Lippert, B.; Scho¨llhorn, H.; Thewalt, U. Inorg. Chim. Acta
1985, 107, 217-222. (e) Szalda, D. J.; Kistenmacher, T. J.; Marzilli, L. G.
Inorg. Chem. 1975, 14, 2623-2629.
(39) Marfurt, J.; Leumann, C. Angew. Chem. 1998, 110, 184-187.
(40) Experiments with shorter mixing times or lower concentrations of
the complex gave no cross-peaks which were distinct enough for integration
and distance calculation.

12006 J. Am. Chem. Soc., Vol. 120, No. 46, 1998
Sigel et al.
Figure 8. Hypothetical H bonding alternative to quartet formation
based on the X-ray crystal structure of 1c. 1H NMR data do not support
such an arrangement.
Figure 7. (a) Two cations trans-[Pt(NH3)2(9-EtG-N7)(1-MeC-N3′)]+
of 1c, forming a H bonded dimer (symmetry operation x - 1/y/z).
Ellipsoids are at the 50% probability level. (b) Cation association via
hydrogen bond formation between N4′H2 of 1-MeC and N1 of 9-EtG
(symmetry operations x - 1/y/z and x + 1/y/z).
Figure 9. Sequence of H bond donor (D) and acceptor (A) sites as
found in the diplatinated quartet formed by trans-[Pt(NH3)2(9-EtG-
N7)(1-MeC-N3′)](C6H2N3O7)‚H2O (1b) (AADD, above) and in trans-
[Pt(NH3)2(9-MeA-N7)(9-MeGH-N7)]2+ and trans-[Pt(NH3)2(1-MeU-
N3′)(9-MeA-N7)]+ (ADAD each, below). No quartet formation is
observed for the sequence ADAD.
(2.86(3) Å and 2.92(3) Å) as well as O2′ of the 1-MeC ligands
(2.95(3) Å and 2.91(3) Å) (Figure 7a). This pattern appears to
be a recurring motif of bis(nucleobase) complexes of trans-
PtII(NH3)2 and has been observed, among others, in trans-
[Pt(NH3)2(1-MeC-N3′)(7,9-DimeG-N1)]2+ 28 as well as in the
protonated form and in a heteronuclear derivative of trans-
Pt(NH3)2(1-MeU)2.41 Second, pairs of stacked cations are
connected by a single short H bond (2.80(1) Å) between N4′
of 1-MeC and N1 of 9-EtG (Figure 7b). There is also a long
contact between C5′ of 1-MeC and O6 of 9-EtG of 3.66(2) Å.
This separation is probably too long to be considered a CH‚‚‚
O hydrogen bond. Typically, C‚‚‚O distances in these H bonds
are in the range of 2.9-3.3 Å.33a However, if a favorable
geometry of the H bond is realized, values of up to 3.9-4.1 Å
are still considered (weak) H bonds.42
Irrespective of such considerations and even assuming that
in solution the C5′(1-MeC)-O6(9-EtG) separation becomes
sufficently short to get the two positions into reach for H
bonding (Figure 8), such an arrangement appears to be unlikely
to explain the solution behavior for the following reasons: (i)
Associates with two H bonds only are virtually never detected
in DMSO-d6 solution, (ii) the involvement of the second proton
of N4′H2 of 1-MeC in H bonding is not accounted for (cf.
above), and (iii) the ESI-MS spectrum (recorded in MeOH)
gives no hint for oligomers, yet clear evidence for a quartet.6
Related Systems. In the course of our studies on “metal-
modified base pairs“ we have prepared also compounds of the
type trans-[Pt(NH3)2(9-MeA-N7)(9-MeGH-N7)]2+ 4a and trans-
[Pt(NH3)2(1-MeU-N3′)(9-MeA-N7)]+.43 On steric grounds these
compounds should likewise be capable of forming metalated
base quartets (Figure 9). However, neither 1H NMR spectra in
DMSO-d6 nor presently available X-ray crystal structure
analyses provide any hint for a dimerization as seen with 1b.
At least in the case of the mixed uracil, adenine complex charge
repulsion cannot account for this difference, since both cations
carry the same +1 charge. What is different between 1b and
the two other complexes, however, is the sequence of donor
(D) and acceptor (A) sites within the mononuclear entities:
While it is AADD in 1b, it is ADAD in the two other
compounds. As has been pointed out by Jorgensen et al.,44
(43) Thompson, S.; Sigel, R. K. O.; Freisinger, E.; Lippert, B. Unpub-
lished results.
(41) Zamora, F.; Witkowski, H.; Freisinger, E.; Albinati, A.; Lippert,
B. submitted for publication.
(42) Steiner, T. J. Chem. Soc., Chem. Commun. 1997, 727-734.
(44) (a) Jorgensen, W. L.; Severance, D. L. J. Am. Chem. Soc. 1991,
113, 209-216. (b) Pranata, J.; Wierschke, S. G.; Jorgensen, W. L. J. Am.
Chem. Soc. 1991, 113, 2810-2819.

Metalated Nucleobase Quartets
J. Am. Chem. Soc., Vol. 120, No. 46, 1998 12007
favorable secondary electrostatic interactions in the quartet
structure of 1b, possible between H5′ of 1-MeC and O6 of 9-EtG
as well as between the intermolecularly bound NH of 1-MeC
and N1 of 9-EtG, might account for an extra stabilization.
NH‚‚‚O commonly found in nucleic acids as well as the rather
novel CH‚‚‚O hydrogen bond38a,b now to CH‚‚‚N. Whether or
not such H bonds involving deprotonated bases are biologically
relevant (e.g., in multistranded nucleic acids; during genetic
recombination; during forced duplex association under the
influence of cross-linking metal ions, etc.) is admittedly unclear.
However, the strength of the association of the base quartet,
which exceeds that of the Watson-Crick pair between gua-
nosine and cytidine by far, is quite remarkable and needs to be
emphasized.
Conclusions
Metal complexes which lead through H bonding interactions
to supramolecular ensembles are receiving increased attention,
for reasons such as crystal engineering, molecular recognition,
or energy transfer.45 Our interest in such systems3,5b,8,46 stems
largely from biological aspects such as the effects of binding
of heavy metal ions to nucleobases to their H bonding properties
with respect to mispairing patterns or the stabilization of
nucleobase associates by an interplay of metal coordination and
H bonding. The here described complex 1b is unique in that it
displays an H-bonding pattern unprecedented in nucleic acid
chemistry involving a CH donor and a negatively charged N
acceptor. It extends the list of H bonds of type NH‚‚‚N and
Acknowledgment. The authors acknowledge support of this
research by the Swiss National Science Foundation and the
Swiss Federal Office for Education and Science (TMR fellow-
ship to R.K.O.S.; No. 83EU-046320), by the Fonds der
chemischen Industrie (fellowship for S.M.), by the Deutsche
Forschungsgemeinschaft, and by Asta Medica.
Supporting Information Available: Tables listing atomic
coordinates, temperature factors, bond lengths and angles, and
torsion angles and details of the refinement of the X-ray
crystallographic data for compounds 1b and 1c (18 pages, print/
PDF). See any current masthead page for ordering information
and Web access instructions.
(45) Burrows, A. D.; Chan, C.-W.; Chowdhry, M. M.; McGrady, J. E.;
Mingos, D. M. P. Chem. Soc. ReV. 1995, 329-339. (b) White, C. M.;
Gonzales, M. F.; Bardell, D. A.; Rees, L. H.; Jeffrey, J. C.; Ward, M. D.;
Armaroli, N.; Calogero, G.; Barigelletti, F. J. Chem. Soc., Dalton Trans.
1997, 727-735. (c) Armaroli, N.; Barigelletti, F.; Calogero, G.; Flamigni,
L.; White, C. M.; Ward, M. D. J. Chem. Soc., Chem. Commun. 1997, 2181-
2182.
(46) Lippert, B. J. Chem. Soc., Dalton Trans. 1997, 3971-3976 and
references cited.
JA981637+