Effects of ligand planarity on the interaction of polypyridyl Ru(II) complexes with DNA

Article abstract of DOI:10.1039/b300353a

Two new polypyridyl ligands containing substituent Br at different positions in the phenyl ring, OBIP {OBIP = 2-(2-bromophenyl)imidazo[4,5-f]-1,10-phenanthroline}, PBIP {PBIP = 2-(4-bromophenyl)imidazo[4,5-f]-1,10-phenanthroline} and their Ru(II) complexes, [Ru(dmp)2(OBIP)]²⁺ 1 and [Ru(dmp)2(PBIP)]²⁺ 2 (dmp = 2,9-dimethyl-1,10-phenanthroline), have been synthesized and charactrized. The binding of the two complexes to calf thymus DNA (CT DNA) has been investigated by spectrophotometric methods, viscosity measurements, as well as equilibrium dialysis and circular dichroism spectroscopy. Theoretical calculations for the two complexes were also carried out applying the density functional theory (DFT) method. The structure of complex 1 has been determined by single-crystal X-ray diffraction techniques. The imidazo[4,5-f]-1,10-phenanthroline moiety is not coplanar with the 2-bromophenyl ring, having a dihedral angle of 48.6 degrees in the OBIP ligand. The twisted conformation has been further confirmed by theoretical calculations, in which this dihedral angle is 48.2 degrees. The theoretical calculations also suggest that the PBIP ligand in complex 2 is essentially planar (dihedral angle is 0.4 degrees). The experimental results show that while complex bonds to CT DNA via a semi-intercalative mode, complex 2 strongly binds to CT DNA than through intercalation. Complex 2 is thus a much better candidate as an enantioselective binder to CT DNA complex 1. Some experimental regularities or trends have been reasonably explained by the theoretical results. These suggest that the planarity of the intercalated ligand has significant effects on the spectral properties and the DNA-binding behavior of the complexes, and that the DFT method can be used effectively to explain and predict some regularities or trends in the interaction of polypyridyl Ru(II) complexes with DNA.

Full text of DOI:10.1039/b300353a

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Effects of ligand planarity on the interaction of polypyridyl Ru(II)
complexes with DNA
Hong Xu,a,b Kang-Cheng Zheng,*a,c Yao Chen,d Yi-Zhi Li,d Li-Jun Lin,a,c Hong Li,e
Pei-Xin Zhangb and Liang-Nian Ji*a,c
a The Key Laboratory of Gene Engineering of Ministry of Education, Zhongshan University,
Guangzhou 510275, P. R. China. E-mail: cesjln@zsu.edu.cn; Fax: 86-20-8403-5497;
Tel: 86-20-8411-0115
b Department of Chemistry and Biology, Normal College, Shenzhen University,
Shenzhen 518060, P. R. China
c Department of Chemistry, Zhongshan University, Guangzhou 510275, P. R. China
d State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093,
P. R. China
e Department of Chemistry, South China Normal University, Guangzhou 510631, P. R. China
Received 10th January 2003, Accepted 10th April 2003
First published as an Advance Article on the web 25th April 2003
Two new polypyridyl ligands containing substituent Br at different positions in the phenyl ring, OBIP {OBIP =
2-(2-bromophenyl)imidazo[4,5-f ]-1,10-phenanthroline}, PBIP {PBIP = 2-(4-bromophenyl)imidazo[4,5-f ]-1,10-
phenanthroline} and their Ru() complexes, [Ru(dmp)2(OBIP)]2ϩ 1 and [Ru(dmp)2(PBIP)]2ϩ 2 (dmp = 2,9-dimethyl-
1,10-phenanthroline), have been synthesized and characterized. The binding of the two complexes to calf thymus
DNA (CT DNA) has been investigated by spectrophotometric methods, viscosity measurements, as well as
equilibrium dialysis and circular dichroism spectroscopy. Theoretical calculations for the two complexes were also
carried out applying the density functional theory (DFT) method. The structure of complex 1 has been determined
by single-crystal X-ray diffraction techniques. The imidazo[4,5-f ]-1,10-phenanthroline moiety is not coplanar with
the 2-bromophenyl ring, having a dihedral angle of 48.6Њ in the OBIP ligand. The twisted conformation has been
further confirmed by theoretical calculations, in which this dihedral angle is 48.2Њ. The theoretical calculations also
suggest that the PBIP ligand in complex 2 is essentially planar (dihedral angle is 0.4Њ). The experimental results show
that while complex 1 binds to CT DNA via a semi-intercalative mode, complex 2 strongly binds to CT DNA through
intercalation. Complex 2 is thus a much better candidate as an enantioselective binder to CT DNA than complex 1.
Some experimental regularities or trends have been reasonably explained by the theoretical results. These suggest
that the planarity of the intercalated ligand has significant effects on the spectral properties and the DNA-binding
behavior of the complexes, and that the DFT method can be used effectively to explain and predict some regularities
or trends in the interaction of polypyridyl Ru() complexes with DNA.
interesting properties upon binding to DNA.7 Thus it is of
interest to delineate the effects of the planarity of the inter-
Introduction
Over the past decade, the interaction between transition metal
complexes and DNA has been extensively studied.1 In recent
years, polypyridyl Ru() complexes have attracted much
attention. As intercalating photoactive electron donors, poly-
pyridyl Ru() complexes have been used to study DNA-
mediated charge transport.2 Some new technologies such as
picosecond time-resolved resonance Raman spectroscopy and
femtosecond linear dichroism spectroscopy have been applied
to study DNA-binding geometries, binding modes and binding
dynamics of polypyridyl Ru() complexes.3 Increasing attention
has also been given to the design of novel polypyridyl Ru()
complexes which may be employed as probes of nucleic acid
structures and sites.4 Polypyridyl Ru() complexes can bind to
DNA in a non-covalent interactive fashion such as electrostatic
binding, groove binding5 and intercalative binding (including
classical intercalation,6 semi-intercalation and quasi-inter-
calation3f). Many important applications of these complexes
require that the complex binds to DNA through an intercalative
mode. Generally the intercalative ligand of polypyridyl Ru()
complex should contain an aromatic heterocyclic functionality
that can insert and stack between the base pairs of double
helical DNA.1 Therefore most of the reported complexes
contain only planar aromatic ligands and investigations of
polypyridyl Ru() complexes with non-planar ligands as
DNA-binding reagents have been relatively few. In fact, some
of the complexes containing non-planar ligand also exhibit
calative ligand on interaction and the binding mode of the
complexes to DNA. In this paper, we selected OBIP {OBIP =
2-(2-bromophenyl)imidazo[4,5-f ]-1,10-phenanthroline}
and
PBIP {PBIP = 2-(4-bromophenyl)imidazo[4,5-f ]-1,10-phenan-
throline} as intercalative ligands. The ortho-Br group shows a
significant steric effect and can interact with N in OBIP,
whereas the space constraint and such an N-interaction of the
para-Br group in PBIP are negligible. As a result, the planarity
of the two ligands could be different by selecting a suitable
ancillary ligand.
To more clearly compare the effects of the planarity of the
intercalative ligand on interaction of a complex with DNA, the
selection of ancillary ligands is also very important. Ancillary
ligands can also indirectly affect the DNA-intercalation state
through changing the planarity of the main ligand. From the
results of previous experiments,8 dmp (dmp = 2,9-dimethyl-
1,10-phenanthroline) can not intercalate into DNA and its
methyl substituents are π-electron-pushing groups. It is with
such considerations that leads us to select dmp as the ancillary
ligands, and the complexes [Ru(dmp)2(OBIP)]2ϩ 1 and [Ru-
(dmp)2(PBIP)]2ϩ 2 were thus selected for study. Since the four
methyl substituents of the two ancillary ligands leads to an
increase of electron density at the N and ortho-Br atoms in the
main ligand OBIP, this will cause an increase of Coulombic
repulsion between N and Br, and as a result, may lead to non-
planarity of OBIP.
D a l t o n T r a n s . , 2 0 0 3 , 2 2 6 0 – 2 2 6 8
T h i s j o u r n a l i s © T h e R o y a l S o c i e t y o f C h e m i s t r y 2 0 0 3
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We report herein the syntheses and characteristics of two
new polypyridyl ligands, OBIP and PBIP, and the corre-
sponding Ru() complexes, [Ru(dmp)2(OBIP)]2ϩ 1 and [Ru-
(dmp)2(PBIP)]2ϩ 2, along with the crystal structure of complex
1 and examine their different DNA-binding behaviors. The
theoretical calculations applying the density functional
theory (DFT) method9 for these two complexes were also
carried out and applied to explain the obtained experimental
observations. This paper is focused on exploring the effects of
intercalated ligand planarity on the DNA-binding behavior and
the spectral properties of the complexes.
[(CD3)2SO]: δ 8.90 (d, 2H), 8.74 (d, 2H), 8.42 (t, 4H), 8.23 (t,
4H), 7.96 (d, 2H), 7.62 (d, 2H), 7.37 (d, 2H), 7.33 (t, 2H), 7.13
Ϫ 2ϩ
(br, 2H), 1.94 (s, 6H), 1.71 (s, 6H). m/z 892 ([M Ϫ 2ClO4 ] ).
The ligand, MBIP {MBIP = 2-(3-bromophenyl)imidazo-
[4,5-f ]-1,10-phenanthroline} and its Ru complex, [Ru(dmp)2-
(MBIP)]2ϩ have also been synthesized with a analogous
procedure described above. Unfortunately, the complex did
not dissolve in water. Thus, unfortunately, we could not system-
atically study the effects of the planarity of the intercalative
ligands containing Br-groups substituted at all the different
position of the phenyl ring, on the binding mode of the
complexes to DNA.
CAUTION: Perchlorate salts of metal complexes with
organic ligands are potentially explosive, and only small
amounts of the material should be prepared and handled with
great care.
Experimental
Syntheses
The complex cis-[Ru(dmp)2Cl2]ؒ2H2O and 1,10-phenanthroline-
5,6-dione were prepared according to the literature pro-
cedures.10 Other reagents and solvents were purchased
commercially and used without further purification unless
otherwise noted.
Crystallography
Crystal data and data collection parameters. C49H39BrClN9-
O5Ru, M = 1050.31, monoclinic, space group P21/c (no. 14),
a = 11.526(1), b = 21.726(2), c = 18.124(1) Å, α = 90.00,
β = 92.12(1), γ = 90.00Њ, U = 4535.4(6) Å3, T = 293 K, Z = 4,
µ(Mo-Kα) = 1.345 mmϪ1, 22331 reflections measured, 7967
unique (Rint = 0.025) which were used in all calculations. The
final wR(F 2) was 0.0799 (all data).
OBIP. OBIP was synthesized by a similar method described
previously.11 A mixture of 2-brombenzaldehyde (3.5 mmol, 0.40
cm3), 1,10-phenanthroline-5,6-dione (2.5 mmol, 0.525 g),
ammonium acetate (50 mmol, 3.88 g) and glacial acetic acid (10
cm3) was refluxed for about 2 h, then cooled to room temper-
ature and diluted with water (ca. 25 cm3). Dropwise addition
of concentrated aqueous ammonia gave yellow precipitates,
which were collected and washed with water. The crude
products were purified by silica gel filtration (60–100 mesh,
ethanol). The principal yellow band was collected. The solvent
was removed by rotary evaporation, the products were
collected, and then dried at 50 ЊC in vacuo. Yield 0.727 g, 78%
(Found: C, 60.57; H, 3.28; N, 14.80%. Calc. for C19H11BrN4: C,
Structure solution and refinement. Single crystal X-ray diffrac-
tion experiments were carried out with a Bruker Smart Apex
CCD area detector in the range 1.87 < θ < 25.00Њ, Ϫ13 ≤ h ≤ 13,
0 ≤ k ≤ 25, 0 ≤ l ≤ 21, operating in ω scan mode and using
graphite-monochromated Mo-Kα radiation (λ = 0.71073 Å).
The reflection intensities were corrected by means of a ψ-scan.
The structure was solved by direct methods and refined by
full-matrix least-squares against F 2 of all data, using the
SHELXTL 97 program.12 All hydrogen atoms were generated
geometrically (C–H 0.96 Å). 624 parameters were applied
to refinement. The final difference map had peaks between
Ϫ0.49 and 0.45 e ÅϪ3.
1
60.80; H, 2.93; N, 14.93%). H NMR [(CD3)2SO]: δ 13.84 (s,
1H), 9.05 (d, 2H), 8.90 (d, 1H), 8.86 (d, 1H), 7.87 (q, 2H), 7.83
(d, 2H), 7.62 (t, 1H), 7.53 (t, 1H). m/z 375 and 377 (Mϩ).
CCDC reference number 195053.
See http://www.rsc.org/suppdata/dt/b3/b300353a/ for crystal-
lographic data in CIF or other electronic format.
PBIP. This compound was obtained using a procedure
analogous to that for OBIP, using 4-brombenzaldehyde in place
of 2-brombenzaldehyde. Yield 0.694 g, 74% (Found: C, 60.69;
H, 3.31; N, 14.89%. Calc. for C19H11BrN4: C, 60.80; H, 2.93; N,
Measurements
1
14.93%). H NMR [(CD3)2SO]: δ 13.56 (br, 1H), 9.03 (d, 2H),
8.92 (d, 2H), 8.25 (d, 2H), 7.82 (m, 4H). m/z 375 and 377 (Mϩ).
Elemental analyses (C, H and N) were carried out with a
Perkin-Elmer 240C elemental analyzer. H NMR spectra were
1
[Ru(dmp)2(OBIP)](OH)(ClO4)ؒCH3CN 1. This complex was
prepared by the following method. A mixture of cis-[Ru-
(dmp)2Cl2]ؒ2H2O (0.5 mmol, 0.321 g), OBIP (0.5 mmol, 0.187
g), ethanol (10 cm3) and water (5 cm3) was refluxed under argon
for 2 h to give a clear red solution. After most of the ethanol
solvent was removed under reduced pressure, a red precipitate
was obtained by dropwise addition of a saturated aqueous
NaClO4 solution. The product was purified by column chrom-
atography on alumina using acetonitrile–toluene (1 : 1 v/v) as
eluent and then dried in vacuo. Red prismatic single crystals
of [Ru(dmp)2(OBIP)](OH)(ClO4)ؒCH3CN were obtained by
evaporating a solution of the complex in acetonitrile–toluene–
water. Yield, 0.331 g, 63% (Found: C, 56.23; H, 3.62; N, 12.30%.
Calc. for C49H39BrClN9O5Ru: C, 56.03; H, 3.72; N, 12.01%). 1H
NMR [(CD3)2SO]: δ 8.99 (d, 2H), 8.81 (d, 2H), 8.51 (t, 5H), 8.33
(d, 2H), 8.06 (d, 2H), 7.94 (d, 1H), 7.81 (d, 1H), 7.54 (t, 1H),
7.46 (d, 2H), 7.42 (m, 3H), 7.23 (br, 1H), 2.04 (s, 6H), 1.81 (s,
6H). m/z 893 ([M Ϫ OHϪ Ϫ ClO4Ϫ Ϫ CH3CN ϩ 1]2ϩ).
recorded on a Bruker DRX-500 NMR spectrometer with
(CD3)2SO as solvent and SiMe4 as an internal standard. An
LCQ electrospray mass spectremeter (ESMS, Finnigan) was
employed for the investigation of charged metal complex
species in methanol solvent. UV-Vis spectra were recorded on
a Shimadzu UV-2501PC spectrophotometer. Emission spectra
were determined with a Shimadzu RF-5301PC fluorescence
spectrometer. The circular dichroism spectra of dialyzates were
measured on a JASCO J-715 spectropolarimeter.
Cyclic voltammetry was performed on an Autolab
PGSTAT30 electrochemical system. The supporting electrolyte
was 0.1 M tetrabutylammonium perchlorate in acetonitrile
freshly distilled from phosphorus pentaoxide. All samples were
purged with nitrogen prior to measurements at room tem-
perature. The electrochemical measurements were made in a
typical cell using a platinum wire working electrode, a platinum
flat counter electrode, and a standard saturated sodium calomel
electrode (SSCE).
All the experiments involving interaction of the complexes
with DNA were conducted in twice distilled buffer containing
tris(hydroxymethyl)aminomethane (Tris, 5 mM) and NaCl (50
mM) and adjusted to pH 7.2 with hydrochloric acid. A solution
of calf thymus DNA in the buffer gave a ratio of UV absorb-
ance at 260 and 280 nm of about 1.8–1.9:1, indicating that the
[Ru(dmp)2(PBIP)](ClO4)2 2. This red complex was synthe-
sized in a manner identical to that described for complex 1,
with 0.5 mmol, 0.187 g PBIP in place of OBIP. Yield, 0.359 g,
66% (Found: C, 52.04; H, 3.42; N, 10.33%. Calc. for
1
C47H35BrCl2N8O8Ru: C, 51.70; H, 3.21; N, 10.27%). H NMR
D a l t o n T r a n s . , 2 0 0 3 , 2 2 6 0 – 2 2 6 8
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DNA was sufficiently free of protein.13 The DNA concentration
per nucleotide was determined by absorption spectroscopy using
the molar absorption coefficient (6600 MϪ1 cmϪ1) at 260 nm.14
For the absorption spectra, equal amounts of DNA were
added to both complex and reference solutions to eliminate the
absorbance of DNA itself. The intrinsic binding constant Kb of
a complex to CT DNA was determined from eqn. (1)15 through
a plot of [DNA]/(εa Ϫ εf) vs. [DNA].
Table 1 Selected bond lengths (Å) and angles (Њ) for [Ru(dmp)2-
(OBIP)](OH)(ClO4)ؒCH3CN 1
Ru–N(1)
Ru–N(2)
Ru–N(3)
2.110(2)
2.092(2)
2.096(2)
Ru–N(4)
Ru–N(5)
Ru–N(6)
2.096(2)
2.073(2)
2.079(2)
N(1)–Ru–N(2)
N(1)–Ru–N(3)
N(1)–Ru–N(4)
N(1)–Ru–N(5)
N(1)–Ru–N(6)
N(2)–Ru–N(3)
N(2)–Ru–N(4)
N(2)–Ru–N(5)
N(2)–Ru–N(6)
N(3)–Ru–N(4)
N(3)–Ru–N(5)
N(3)–Ru–N(6)
N(4)–Ru–N(5)
N(4)–Ru–N(6)
79.54(10)
178.45(9)
101.90(9)
98.65(9)
82.24(9)
100.19(9)
94.56(9)
173.18(8)
94.34(8)
79.63(9)
81.43(9)
96.27(9)
92.25(8)
170.74(8)
N(5)–Ru–N(6)
Ru–N(1)–C(1)
Ru–N(1)–C(12)
Ru–N(2)–C(10)
Ru–N(2)–C(11)
Ru–N(3)–C(15)
Ru–N(3)–C(26)
Ru–N(4)–C(24)
Ru–N(4)–C(25)
Ru–N(5)–C(38)
Ru–N(5)–C(39)
Ru–N(6)–C(29)
Ru–N(6)–C(40)
78.88(8)
130.7(2)
109.9(2)
130.9(2)
111.30(19)
132.12(19)
110.66(18)
130.9(2)
111.09(17)
128.32(18)
114.91(16)
128.90(19)
113.96(16)
(1)
where [DNA] is the concentration of DNA in base pairs, εa, εf
and εb are, respectively, the apparent extinction coefficient (Aobs
/
[M]), the extinction coefficient for free metal (M) complex and
the extinction coefficient for the metal (M) complex in the fully
bound form. In plots of [DNA]/(εa Ϫ εf) vs. [DNA], Kb is given
by the ratio of the slope to the intercept.
For the steady-state competitive binding experiment, accord-
ing to the classical Stern–Volmer equation (2)16
Io/I = 1 ϩ Kr
(2)
where I0 and I are the fluorescence intensities in the absence
and presence of complex, respectively. K is a linear Stern–
Volmer quenching constant dependent on the ratio of the
bound concentration of ethidium bromide (EB) to the concen-
tration of DNA; r is the ratio of the total concentration of the
complex to that of DNA ([Ru]/[DNA]). In the plot of I0/I vs. r,
the Stern–Volmer quenching constant K is given by the ratio of
the slope to the intercept.
Viscosity measurements were carried out using an Ubbdlodhe
viscometer maintained at a constant temperature of 28.0
0.1 ЊC in a thermostatic bath. DNA samples with an approx-
imate average length of 200 base pairs were prepared by sonica-
tion in order to minimize complexities arising from DNA
flexibility.17 Flow time was measured with a digital stopwatch.
Each sample was measured three times and an average flow
time was calculated. Data are presented as (η/η0)1/3 vs. binding
ratio ([Ru]/[DNA]),18 where η is the viscosity of DNA in the
presence of complex and η0 is the viscosity of DNA alone.
Viscosity values were calculated from the observed flow time of
DNA-containing solutions (t > 100 s) corrected for the flow
time of buffer alone (t0), η = t – t0.
Fig. 1 An ORTEP drawing of [Ru(dmp)2(OBIP)]2ϩ and the atom
numbering.
[Ru(dmp)2(OBIP)]2ϩ cation, a disordered ClO4Ϫ, a OHϪ and an
acetonitrile molecule. The OHϪ anion forms a hydrogen bond
with the imidazole nitrogen (N7). An ORTEP drawing of the
cation with atomic numbering scheme is depicted in Fig. 1.
Selected bond lengths and angles are summarized in Table 1.
The theoretical calculations for these two complexes have also
given some structural parameters which are listed in Table 2.
As shown in Fig. 2, the central Ru() atom is chelated by two
dmp ligands oriented in a cis geometry and a OBIP ligand. The
average Ru–N bond length (2.091 Å) is comparable with those
published for [Ru(phen)3]2ϩ (2.063 Å),24 although there are
some differences in size and shape among phen, dmp and OBIP.
The coordination geometry about the Ru() atom is that of a
distorted octahedron, with a bite angle of 79.35Њ averaged over
the three bidentate ligands. Of most interest is the configuration
of the expected DNA-intercalating ligand OBIP in the com-
plex. We noticed that, to minimize possible steric interaction
between the substituent Br group and the imidazole ring, the
2-bromophenyl group is remarkably twisted with respect to the
imidazo[4,5-f ]-1,10-phenanthroline plane forming a dihedral
angle of 48.6Њ. This twisted conformation has also been
confirmed by theoretical calculations, in which this dihedral
angle is 48.2Њ.
The dialysis membrane was purchased from Union Carbide
Co. and treated by means of the general procedure before use.19
Equilibrium dialysis was carried out in the dark and held at 4 ЊC
for 48 h with 5 cm3 of calf thymus DNA (1.0 mM) sealed in a
dialysis bag and 10 cm3 of the complex (100 µM) outside the bag.
Theoretical calculations
Each of these two complexes forms from a Ru() ion, one main
(intercalating) ligand (PBIP or OBIP) and two ancillary ligands
(dmp). Full geometry optimization computations were pre-
formed applying the DFT-B3LYP method9 and LanL2DZ
basis set,20 and assuming the singlet state for the complexes.21
All computations were performed with the G98 quantum chem-
istry program-package.22 In order to vividly depict the detail of
the frontier molecular orbital interactions, the stereographs of
some related frontier molecular orbitals of the complexes were
drawn with the Molden v3.6 program23 based on the obtained
computational results.
For complex 2, since the Br group substitutes at the para-
position of the phenyl ring in PBIP, it has a negligible steric
influence on the coplanarity of the phenyl containing the
para-Br group and the imidazo[4,5-f ]-1,10-phenanthroline
moiety in PBIP, the expected DNA-intercalating ligand PBIP
should be essentially planar. Results from theoretical calcu-
lations show that this dihedral angle is 0.4Њ. By contrast, in the
complex [Ru(phen)2(OBIP)]2ϩ, the computed results show that
OBIP is planar and thus phen is not an suitable ancillary ligand
Results and discussion
Structures
The molecular structure of complex 1 has been confirmed
by single crystal X-ray diffraction analysis. It consists of a
D a l t o n T r a n s . , 2 0 0 3 , 2 2 6 0 – 2 2 6 8
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Table 2 Computed selected bond lengths (Å) and angles (Њ) of the complexes
OBIP or PBIP
dmp
Compound
Ru–N
N–Ru–N
C–C/C–N
C–Br
Ru–N
N–Ru–N
C–C/C–N
ꢀa/Њ
1
2
2.126
2.125
78.5
78.5
1.405
1.405
1.962
1.951
2.155
2.156
79.1
79.0
1.407
1.407
48.1521
0.4008
a ꢀ = Dihedral angle between the benzene and imidazole ring of the intercalative ligand.
Fig. 2 1H NMR spectra of the aromatic region of complex 1 (top) and complex 2 (bottom).
to induce non-coplanarity. Our design strategy was thus
confirmed by the single crystal X-ray diffraction analysis and
theoretical calculations on 1.
owing to the repulsive interaction between two methyl substit-
uents of each dmp ligand, along with the consideration that the
PBIP ligand in complex 2 is more symmetrical than the OBIP
ligand in complex 1, the chemical shifts of the protons located
in the phenanthroline ring of dmp are totally split in complex 1
but only partially split in complex 2. The proton resonance
signals of the phenanthroline moiety for the OBIP ligand in
complex 1 appear to more downfield in comparison with those
of PBIP ligand in complex 2. This relates to the structure of the
ligands. Since the conformation of the OBIP ligand in complex
1 is twisted by 48.6Њ, the protons located in the phenanthroline
moiety of OBIP ligand suffer a stronger π-attraction from N
atoms with greater electronegativity, and thus these protons
possess more positive charge. As a result they are more down-
field shifted.
The crystallography as well as DFT calculations of the
complexes refer to conditions in the absence of DNA. At
the present time, we are not yet able to determine and calcu-
late the structure of a supermolecular system formed from
DNA and a complex by crystallography as well as DFT calcu-
lations. However, since we have determined and calculated
the structures of the complexes in the absence of DNA by reli-
able methods, it is reasonable to research the trends in DNA-
binding of the complexes and analyze the relations between the
structures of the free complexes and their DNA-binding
properties. Such results should be useful theoretical
benchmarks.
1H NMR spectra
Electrochemistry
The 1H NMR spectra of complexes 1 and 2 are shown in Fig. 2.
Considering the influence of steric, inductive and conjugative
effects sytematically and comparing them with those of similar
compounds,25 all proton resonance signals of the aromatic
region are assigned and given in Fig. 2. For each of the two
complexes, two sets of NMR signal were observed. One set
corresponds to the dmp ligand, and the other set corresponds
to the OBIP or PBIP ligand. Both the two complexes display
approximate C2v symmetry in solution, and the two dmp
ligands and the two halves of OBIP or PBIP have nearly the
same chemical and magnetic environment. On the other hand,
The electrochemical behavior of the two complexes have been
studied in acetonitrile. The cyclic voltammetric (CV) behavior
of complexes 1 and 2 are shown in Fig. 3. Each complex exhibits
well shaped oxidation (one) and reduction (two) waves in the
sweep range from Ϫ1.9 to ϩ1.7 V, the half-wave potentials E1/2
,
taken as the average of the cathodic peak potential Epc and the
anodic peak potential Epa, being Ϫ1.671, Ϫ1.438 and 1.322 V
vs. SCE for [Ru(dmp)2(OBIP)]2ϩ and Ϫ1.681, Ϫ1.438 and 1.330
V for [Ru(dmp)2(PBIP)]2ϩ. A small, poorly shaped reduction
wave appears at ca. Ϫ1.065 and Ϫ1.087 V for [Ru(dmp)2-
(OBIP)]2ϩ and [Ru(dmp)2(PBIP)]2ϩ, respectively.
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Table 3 Some frontier molecular orbital energies (εI/atomic unit) of the complexes (1 atomic unit = 27.21 eV)
Compound
Occ
Occ
NHOMO
HOMO
LUMO
Vir
∆εL–H
∆εL-NH
1
2
Ϫ0.3932
Ϫ0.3994
Ϫ0.3881
Ϫ0.3911
Ϫ0.3872
Ϫ0.3883
Ϫ0.3744
Ϫ0.3649
Ϫ0.2641
Ϫ0.2648
Ϫ0.2622
Ϫ0.2627
0.1103
0.1001
0.1231
0.1235
1
Fig. 4 Schematic diagram of energies and related MLCT transitions
of complexes 1 and 2.
Absorption spectroscopic studies
The electronic absorption spectra of complexes 1 and 2 mainly
consist of two resolved bands. The low energy absorption band
centered at ∼470 nm is assigned to a metal-to-ligand charge
transfer (MLCT) transition and the other band centered at
∼270 nm is attributed to an intraligand (IL) π–π* transition by
comparison with the spectra of other polypyridyl Ru() com-
plexes.21 The electronic spectral traces of the two complexes
titrated with DNA are shown in Fig. 6. As the DNA con-
centration is increased, for complex 1, the hypochromism in
the IL band reaches as high as 15.9% at 269 nm with a red shift
of 1 nm at a ratio of [DNA]/[Ru] of 9. The MLCT band at
465 nm shows hypochromism by about 7.7% and a red shift of
2 nm under the same experimental conditions. For complex 2,
upon addition of DNA, the IL band at 271 nm exhibits
hypochromism of about 26.0% with a 4 nm red shift at a ratio
of [DNA]/[Ru] of 6. Although the MLCT band at 466.0 nm
shows no obvious hypochromism, a red shift of 9 nm in the
MLCT band is observed under the same experimental con-
ditions. Comparing the hypochromism of the two complexes
with that of their parent complex [Ru(phen)3]2ϩ (hypochromism
of 12% in the MLCT band at 445 nm and red shift of 2 nm),28
which interacts with DNA through a semi-intercalation or
quasi-intercalation,3f and considering that the absorption
spectrum of [Ru(bpy)3]2ϩ, a typical electrostatic binding com-
plex, was demonstrated to be unchanged upon the addition of
the DNA,5a these spectral characteristics obviously suggest that
the two complexes in our paper interact with DNA most likely
through a mode that involves a stacking interaction between the
aromatic chomophore and the base pairs of DNA. The spectra
also imply that complex 2 binds to DNA more strongly than
complex 1.
Fig. 3 Cyclic voltammogram of complex 1 (top) and complex 2
(bottom).
The electrochemical behavior of Ru() polypyridyl complex
has been rationalized in terms of a metal-based oxidation and
a series of reductions, which are based on the ligands and
occur in a stepwise manner for each π* system.26 As expected,
the oxidation potential of [Ru(dmp)2(PBIP)]2ϩ is 8 mV more
positive than that of [Ru(dmp)2(OBIP)]2ϩ. The phenyl ring
containing the para-Br group is coplanar with the imidazo-
[4,5-f ]-1,10-phenanthroline moiety in PBIP, which expands the
π-delocalization and thus decreases the σ-donor capacity of
PBIP, leading to a decrease of the electron density on the Ru
ion, and in turn stabilizes the metal dπ orbital.27 As a result, the
oxidation potential shifts more positively. The first reduction,
which depends on the ligand predominantly populated by the
lowest unoccupied molecular orbital (LUMO),26 is proposed
to occur at PBIP or OBIP, and appears irreversible, making
a comparison between the two complexes difficult. The latter
two successive reductions are characteristic of the two dmp
ligands.26
The above-mentioned electrochemical trends can be also
explained by our theoretical results. Some computed frontier
MO energies, schematic diagram of energies, and the related
orbital stereograghs of the two complexes are given in Table 3,
Fig. 4 and Fig. 5, respectively. From Fig. 5, we can see that the
MO characterized by metal d-orbitals in the occupied frontier
MO is the NHOMO instead of HOMO, so that the oxidation
of the central metal should happen on the NHOMO. Since the
NHOMO energy of complex 2 is lower than that of complex 1
(see Table 3 and Fig. 4), its oxidation potential is more positive
than that of the latter. On the other hand, since the LUMO is
playing an electron-accepting role, and the LUMO energy of
complex 2 is also lower than that of complex 1, the reduction
potential of the former is more negative than that of the latter.
To compare quantitatively the affinity of the two complexes
towards DNA, the intrinsic binding constants Kb of the two
complexes to CT DNA were determined by monitoring the
changes of absorbance in the IL band with increasing concen-
tration of DNA. The intrinsic binding constant Kb of com-
plexes 1 and 2 obtained were ca. 1.18 × 104 and 3.12 × 104 MϪ1
,
respectively, from the decay of the absorbances. Comparing the
intrinsic binding constant of the two complexes with those of
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Fig. 5 Some related frontier molecular orbital stereographs of complexes 1 and 2.
29
DNA-intercalative Ru() complexes (1.1 × 104–4.8 × 104 MϪ1
)
and the parent complex [Ru(phen)3]2ϩ (5.5 × 103 MϪ1),7b we can
deduce that complex 2 binds strongly to DNA by intercalation
and complex 1 is on the border of classical intercalation and
near non-classical intercalation to DNA. The better binding of
complex 2 to DNA than that of complex 1 can be explained by
the the better planarity of the PBIP ligand in complex 2 than
that of OBIP ligand in complex 1. The intrinsic binding
constants of both the complexes are smaller than that of [Ru-
(dmp)2(HPIP)]2ϩ {HPIP = 2-(2-hydroxyphenyl)imidazo[4,5-f ]-
1,10-phenanthroline} (4.0 × 105 MϪ1),30 and much smaller than
that of [Ru(dmp)2(dppz)]2ϩ (dppz = dipyridophenazine) (2.3 ×
106 MϪ1).31 This can also be interpreted by the planarity of the
intercalated ligand. For the HPIP ligand, the ortho phenolic
group of HPIP could be closely coplanar with the imidazole
ring due to the formation of an intramolecular hydrogen bond
with the nitrogen atom of the imidazole ring.32 The planar area
and the size of the extended π system for the intercalated
ligands is in the order of dppz > HPIP > PBIP > OBIP. In
general, extension of the intercalative ligand planarity will
increase the strength of interaction of the complexes with
DNA.33
the experimental wavelength (λmax), using ∆εL–H data of related
complexes in Table 3 and selecting the parent complex
[Ru(bpy)3]2ϩ as the standard (λmax = 452, ∆εL–H = 0.1239 atomic
1
unit),34 we can evaluate the wavelengths λmax of the MLCT
bands of complexes 1 and 2 to be ∼455 nm, cf. the experimental
value of ∼465 nm. In addition, the binding constant Kb (2) > Kb
(1) can be also explained by the fact that the LUMO energy
(Ϫ0.2648 atomic unit) of complex 2 is lower than that (Ϫ0.2641
atomic unit) of complex 1. A lower LUMO energy is advan-
tageous to accept the electrons from base pairs of DNA in
intercalative mode according to frontier molecular orbital
theory.
Fluorescence spectroscopic studies
For both the complexes, no emission was observed either in Tris
buffer or in the presence of CT DNA. This could be caused by
vibronic coupling between the methyls of the 2,9-dimethyl-
1,10-phenanthroline ligand and solvent, leading to dissipation
of energy in a non-radiative process. Similar results have
observed for this type of Ru() complexes.30,31
Steady-state competitive binding experiments using com-
plexes 1 and 2 as quenchers may give further information about
the binding of the two complexes to DNA. Ethidium bromide
(EB) emits intense fluorescence light in the presence of DNA,
due to its strong intercalation between adjacent DNA base
pairs. It was previously reported that the enhanced fluorescence
can be quenched, at least partially, by the addition of a second
molecule.16,35 The quenching extent of fluorescence of EB
bound to DNA is used to determine the extent of binding of
the second molecule to DNA. The emission spectra of EB
bound to DNA in the absence and the presence of both the
complexes are shown in Fig. 7. The addition of complexes 1 and
Some trends in electronic absorption spectra can be
explained by the theoretical results. From Fig. 5, we have seen
that the MO characterized by metal d-orbitals in the occupied
frontier MO is NHOMO instead of HOMO, so that the λmax of
1
the MLCT spectral band should be assigned to the electron
transition from the NHOMO to the LUMO. Such an assign-
ment can be confirmed by the fact that the wavelength corre-
1
sponding to the theoretical maximum of the MLCT spectral
band agrees well with the experimental value. According to the
approximate correlation of the reverse ratio of the energy
difference (∆εL–NH) between the LUMO and the NHOMO to
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Fig. 7 Emission spectra of EB bound to DNA in presence of complex
1 (top) and complex 2 (bottom). [EB] = 20 µM, [DNA] = 100 µM; [Ru]/
[DNA] = 0, 0.05, 0.10, 0.15, 0.20, 0.25. The arrows show the intensity
changes upon increasing concentrations of the complexes.
Fig. 6 Absorption spectral of complex 1 (top, [Ru] = 10 µM; [DNA]/
[Ru] = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9) and complex 2 (bottom, [Ru] = 10 µM;
[DNA]/[Ru] = 0, 1, 2, 3, 3, 5, 6) in Tris-HCl buffer upon addition of CT
DNA with subtraction of the DNA absorbance. The arrows show the
absorbance changes upon increasing DNA concentrations. Inset: plots
of [DNA]/(εa Ϫ εf) vs. [DNA] for the titration of DNA with complexes;
᭿, experimental data points; full line, linear fitting of the data.
2 to DNA, pretreated with EB, causes appreciable reduction in
emission intensity of 59.4 and 38.4% relative to that observed
in the absence of complexes 1 and 2 at a ratio of [Ru]/[EB] of
1.25. This indicates that the two complexes compete with EB
in binding to DNA and that DNA-binding of complex 2 is
stronger than that of complex 1.
The fluorescence quenching curves of DNA-bound EB by
complexes 1 and 2 are shown in Fig. 8. The quenching plots
illustrate that the quenching of EB bound to DNA by both
complexes are in good agreement with the linear Stern–Volmer
equation. This proves that the two complexes can bind to DNA.
The Stern–Volmer constant K values for complexes 1 and com-
plex 2 are 2.72 and 5.98, respectively, reflecting the higher
quenching efficiency of complex 2 relative to that of complex 1.
This result suggests DNA-binding of complex 2 is stronger
than that of complex 1. Such a trend is consistent with the
previous absorption spectral results.
Fig. 8 Fluorescence quenching curve of DNA-bound EB by complex
1 (ꢀ) and complex 2 (᭿). [EB] = 20 µM, [DNA] = 100 µM; [Ru]/[DNA]
= 0, 0.05, 0.10, 0.15, 0.20, 0.25.
separated to accommodate the bound ligand, leading to the
increase of DNA viscosity. In contrast, a semi-intercalation
of complex such as ∆-[Ru(phen)3]2ϩ could bend (or kink) the
DNA helix, reduce its effective length and, concomitantly, its
viscosity.3f,36 In addition, some complexes such as [Ru(bpy)3]2ϩ
,
Viscosity studies
which interacts with DNA by an electrostatic binding mode,
Optical photophysical probes generally provide necessary, but
not sufficient clues to support a binding model. Hydrodynamic
measurements that are sensitive to length change (i.e. viscosity
and sedimentation) are regarded as the least ambiguous and
most critical tests of a binding model in solution in the absence
of crystallographic structural data.36 A classical intercalation
model demands that the DNA helix lengthens as base pairs are
have no influence on DNA viscosity.32
The effects of complexes 1 and 2 on the viscosity of DNA are
shown in Fig. 9. The viscosity of DNA decreases with increasing
concentration of complex 1. In contrast, as the amount of
complex 2 is increased, the relative viscosity of DNA increases
steadily. The experimental results suggest that complex 1 binds
to DNA by the non-classical semi-intercalation model and
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dialysate for complex 1 (full lines) shows two CD signals with
a positive peak at 270.6 nm and a negative peak at 246.7 nm,
while complex 2 (dotted lines) shows strong CD signals with a
positive peak at 271.2 nm and a negative peak at 243.0 nm,
respectively. That the CD signals of complex 2 are much
stronger than those of complex 1 is explained by the fact that
complex 2 binds to DNA more strongly than complex 1.
Although neither of the two complexes have been resolved
into their pure enantiomers, and we can not determine which
enantiomer binds to DNA enantioselectively for each of the
two complexes, it is certain that both the two complexes interact
with CT DNA enantioselectivly, and that complex 2 is a much
better candidate for an enantioselective binder to CT DNA
than complex 1.
Conclusions
Fig. 9 Effect of increasing amounts of complex 1 (ꢀ) and complex 2
(᭿) on the relative viscosity of calf thymus DNA at 28.0
[DNA] = 0.5 mM.
0.1 ЊC.
The structure of complex 1 has been determined by single-
crystal X-ray diffraction techniques. The imidazo[4,5-f ]-1,10-
phenanthroline moiety is not coplanar with the 2-bromophenyl
ring, having a dihedral angle of 48.6Њ in OBIP. The twisted
conformation has been further confirmed by theoretical calcu-
lations applying the density functional theory (DFT) method,
in which this dihedral angle is 48.2Њ. The theoretical calcu-
lations also show that the PBIP ligand in complex 2 is essen-
tially planar (the dihedral angle is 0.4Њ). The experimental
results show that while complex 1 binds to CT DNA via a
semi-intercalative mode, complex 2 can strongly bind to CT
DNA through intercalation, and thus complex 2 is a much
better candidate as an enantioselective binder to CT DNA than
complex 1. Some experimental regularities or trends can also
be explained reasonably by the theoretical calculations. All
of these further suggest that the planarity of the intercalated
ligand has a significant effects on the spectral properties, the
DNA-binding behavior and other properties of the complexes,
and that the density functional theory (DFT) method can be
used to explain and predict some regularities or trends in the
interaction of the polypyridyl Ru() complexes with DNA.
complex 2 binds to DNA through a classical intercalation
mode. This difference of DNA-binding mode between com-
plexes 1 and 2 should be caused by the different planarity of the
two complexes. For complex 1, owing the steric constraint of
the ortho-Br group in the phenyl ring, the imidazo[4,5-f ]-1,10-
phenanthroline moiety is not coplanar with the 2-bromophenyl
ring, and the OBIP ligand can not completely intercalate, at
most it could penetrate its substituted phenyl moieties into the
DNA base pairs, leaving the other part of the ligand in the
groove. The semi-intercalation may act as a “wedge” to pry
apart one side of a base-pair stack, as observed for ∆-
[Ru(phen)3]2ϩ 3f,36
but not fully separate the stack as required by
,
the classical intercalation mode. This would cause a static bend
or kink in the helix and decrease the viscosity of DNA. For
complex 2, the intercalated PBIP ligand is essentially planar,
and can intercalate deeply and tightly into adjacent DNA base
pairs. This would cause an extension in the helix and increase
the viscosity of DNA.
Enantioselective binding
Acknowledgements
According to the proposed binding model,37 the ∆ enantiomer
of the complex, a right-handed propeller-like structure, will
display a greater affinity than the Λ enantiomer with the
right-handed calf thymus DNA helix, due to the appropriate
steric matching. The enantiospecific binding of a complex to
DNA can be observed clearly from circular dichroism spectra.
The CD spectra in the UV region of the two complexes after
their racemic solution have been dialysed against CT DNA
are shown in Fig. 10. The presence of CD signals indicates
enrichment of the isomer binding less favorably to DNA. The
We are grateful for the support of the National Natural Science
Foundation of China, the Research Fund of Royal Society of
Chemistry U. K., the Natural Science Foundation of Guang-
dong Province, the State Key Laboratory of Coordination
Chemistry in Nanjing University and the State Key Laboratory
of Bio-organic, Natural Products Chemistry in Shanghai
Institute of Organic Chemistry.
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