The document summarizes a study that used synchrotron X-ray diffraction to analyze the crystal structures of the complexes [Ru(biq)2dpb](PF6)2 and [Ru(biq)2(CH3CN)2](PF6)2. Upon photolysis, [Ru(biq)2dpb](PF6)2 loses its dpb ligand to form [Ru(biq)2(CH3CN)2](PF6)2. This causes a change in coordination geometry around the Ru(II) metal center from nearly spherical to more planar. The planar structure allows for π-π interactions between ligands and increased potential for binding DNA, making these complexes promising

1. Synchrotron X-Ray Diffraction Study of the Products and Reactants associated with the Photocatalytic
Decomposition of [Ru(biq)2dpb](PF6)2 into [Ru(biq)2(CH3CN)2](PF6)2
Amber Harding1, Allen G. Oliver2, Jeanette Krause3, Kaitlyn Wyland1,Avijita Jain1 and Charles H. Lake1
1Department of Chemistry, Indiana University of Pennsylvania, Indiana, PA 15705
2 Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556
3Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221
[Ru(biq)2dpb](PF6)2 is a sterically strained complex where the Ru(II) metal center is protected
by the “spherical” arrangement of three bidentate ligands. Upon photolysis, the complex
undergoes photoinduced ligand exchange releasing the 2,3-bis(2-pyridyl)benzoquinoxaline
(dpb) ligand. Once this ligand is lost, the Ru(II) metal center becomes potentially active for
DNA binding similar to that of cisplatin.
The synthetic pathway for [Ru(biq)2dpb](PF6)2
Crystals of [Ru(biq)2dpb](PF6)2 were grown by vapor
diffusion from a dichloromethane – ether mixture.
These crystals crystallized crystallized in the
monoclinic crystal system P21/c. 12,908 unique
reflections were evaluated. The refinement converged
with R= 3.22% and GOOF= 1.014.
Crystals of [Ru(biq)2(CH3CN)2](PF6)2●2CH3CN were
grown by vapor diffusion from a acetonitrile – ether
mixture. Two acetonitrile solvent molecules were
incorporated in the crystal structure. These crystals
crystallized in the triclinic crystal system P1. 11,213
unique reflections were evaluated. The refinement
converged with R= 3.71% and GOOF= 1.041.
Strained metal complexes such as the strained Ru(II) complexes bind with DNA under
hypoxic conditions, similar to cisplatin.
Ru
N
N
N
N
N
N
hν
Ru
N
N
N
N
solvent
solvent
DNA Ru
N
N
N
N
D
N
A
Ru
N
N
N
N
N
N
hν
Ru
N
N
N
N
solvent
solvent
DNA Ru
N
N
N
N
D
N
A
J. Am. Chem. Soc. 2012, 134, 20, 8324.
Photochem. & Photobiol. Sci. 2014, 13, 272.
Photodynamic therapy is a treatment in which activation of a sensitizer by light of an
appropriate wavelength leads to the destruction of cancer cells by damaging DNA.
.
Aim of SCrALS Program:
Provide access to synchrotrons, for performing small molecule, single-crystal, service
crystallography (i.e. chemical crystallography) that normally cannot be adequately analyzed
by in-house X-ray systems. Service crystallographers and structural scientists who have little
or no access to these facilities.
Methodology & Success:
Mail-in service. Diffraction data is collected
by experienced crystallographers at
ALS Beamline 11.3.1.
Data is then forwarded to the submitters for structure solution & refinement. To date,
samples have been analyzed for researchers representing > 85 institutions ranging from small,
predominately undergraduate colleges to large, graduate research universities.
Complex [Ru(biq)2dpb](PF6)2 [Ru(biq)2(CH3CN)2](PF6)2
Radiation 0.7749 Å 0.7749 Å
Temperature of data
collection
123.15 K 150 K
Space group P21/c
a 9.8299(8) Å 12.7283(11) Å
b 26.790(2) Å 13.9827(12) Å
c 20.1314(16) Å 14.7985(12) Å
α 900 104.965(2)0
β 102.178(2)o 107.819(2)0
γ 900 104.719(2)0
Volume 5182.1(7) Å3 2257.9(3) Å3
Crystal Size 0.04 x 0.035 x
0.015 mm
0.04 x 0.025 x 0.02 mm
Reflections collected 107680 46413
Independent reflections 12908 11213
Data/ Parameters 12908/734 11213/607
GOOF 1.014 1.041
R-factor (2σ) 0.0322 0.0371
R index (all data) 0.0451 0.0483
Largest difference peak
hole
-0.53 eÅ-3 -0.70 eÅ-3
P21/c
[Ru(biq)2dpb](PF6)2
P1
[Ru(biq)2(CH3CN)2](PF6)2
[Ru(biq)2dpb](PF6) 2
[Ru(biq)2(CH3CN)2](PF6)2
The arrangement of the ligands are of particular importance. In [Ru(biq)2dpb](PF6)2 ,one biquinone (biq) ligand is
perpendicular to the other two bidentate ligands (77.10 and 88.20). The two bidentate ligands (biq, dpb) are offset
29.50 from each other. Overall, this complex forms a roughly spherical arrangement. There are no close
intermolecular contacts between complexes. No π- π interactions were observed. This is due to the “spherical”
nature of the complex.
Upon photolysis, the complex loses a less sterically strained dpb ligand forming [Ru(biq)2(CH3CN)2](PF6)2. The two
biq ligands adopt a nearly planar geometry (20.50). This shifting of the biq-ligands to a planar arrangement distorts
the octahedral geometry of the Ru(II) metal center opening a relatively large “bite-angle” for potential
coordination of DNA.
This diagram shows the superposition of the primary coordination geometries of
the Ru(II) metal centers. In the more sterically strained [Ru(biq)2dpb](PF6)2 (blue)
shows only small deviations from true octahedral symmetry. This is the result of
the steric forces of the three bidentate ligands overwhelming any contribution
from π- π interactions. Upon loss of the bidentate dpb ligand due to photolysis,
the steric factors are reduced allowing increased importance of π- π interactions.
This causes a distortion of the primary coordination sphere as the “planar” biq
ligands slide over one-another to maximize these interactions. It is interesting
the less sterically hindered structure possesses significantly more distortion in
the primary coordination sphere.
The biqunione ligands associated with the less sterically hindered
[Ru(biq)2(CH3CN)2](PF6)2 show significant signs of static disorder.
Analysis of these elongated displacement parameters show a
smearing of the electron density at these locations.
This is thought to occur due to the aromatic nature of the biq
ligands. The phenyl rings align due to π- π interactions. There are
numerous possibilities for alignment of the various rings allowing
for many different arrangements through the unit cells of the
crystal structure. What is observed is the averaging of these
structures thus, causing the apparent smearing of the electron
density. Dynamic vibration of the biq ligand may also be a factor.
This is not observed in the more hindered [Ru(biq)2dpb](PF6)2
structure for steric strain dominates the π- π interactions.
The packing diagram of [Ru(biq)2dpb](PF6)2 shows the spherical nature
of the complex. This compound crystallizes in a typical structure
pattern for these types of geometries. No π- π intermolecular contacts
were observed 4.5 Å. Only one intramolecular π- π interaction contact
was noted (at 3.732 Å between the biq and dpb ligands).
This system may be of use for photodynamic therapy and may have advantages for binding DNA. Before photolysis
the complex adopts a nearly spherical geometry protecting the Ru(II) metal center preventing any interaction with
DNA. Upon photolysis, the bidentate ligand with the least steric strain is lost. This may seem counter intuitive at first
but, upon close observation it appears that the ligand is lost so that the complex can maximize π-π interactions. The
intramolecular π-π interactions squeeze the biq ligands together allowing a larger area of the Ru(II) metal center to
be available for binding DNA.
Upon photolysis, the structure adopts a more planar geometry.
This results in "stacks" of molecules maximizing both inter- and
intra-molecular π- π interactions. Notice the channels of PF6 and
CH3CN solvent molecules which surround each “stack”.
The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy
Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231
hѵ
The crystals that were harvested through vapor
diffusion were too small for conventional X-ray
analysis and those from the sterically strained
[Ru(biq)2dpb](PF6)2 complex showed signs of decay in
the X-ray beam. This made the X-ray study an ideal
candidate for the SCrALS program.
reciprocal space plot
showing the c-glide.
+h
+l
0.50 eA-3 contours
This is a “close up” of the stacked [Ru(biq)2(CH3CN)2](PF6)2 complex. There are
three intramolecular π- π interactions less than 4.5 Å ranging from 3.487 Å to
3.800 Å. The “tilt” angles associated with the π-systems range from 25.60 – 31.00.
Seven intermolecular π- π interactions have been observed less than 4.5 Å,
ranging from 3.601 Å to 3.965 Å. The associated “tilt” angles range from 0.00 –
9.10. The increased planarity between the intermolecular π-systems is probably
stronger. Attempting to maximize the wide array of inter- and intra-molecular π-
π interactions probably accounts for the observed disorder in the electron
density map. (For reference the interlayer distance in graphite is 3.41 Å).
Structure Solution: Bruker SHELXTL v5 Program Package.
Structure Refinement: OLEX2-1.1, Dolomanov,, Bourhis, Gildea, Howard, Puschmann J. Appl. Cryst., 42, 339-341.
Graphics Rendering: GIMP-2, Kimball, Mattis et al.
Disorder in the Bidentate Ligands Associated with [Ru(Biq)2(CH3CN)2](PF6)2 due to π- π
interactions
Photodynamic Therapy (PDT)
The Potential Use of [Ru(biq)2dpb](PF6)2 and
[Ru(biq)2(CH3CN)2](PF6)2 for PDT
The SCrALS Project
X-Ray Diffraction Data
Crystal Structures
Change in Coordination Geometry around the Ru(II) metal center
Packing Diagrams and π- π interactions
Conclusions
Acknowledgements
3.801 Å
Tilt = 5.10
3.661 Å
Tilt = 9.10
3.801 Å
Tilt = 5.00
3.661 Å
Tilt = 9.10
3.715 Å
Tilt = 25.70
3.487 Å
Tilt = 25.60
3.800 Å
Tilt = 31.00
3.638 Å
Tilt = 8.20
3.965 Å
Tilt = 0.00
3.638 Å
Tilt = 7.90
RuCl3 x H2O + 2 DMF
Δ 1 hr
+
1. EtOH +H2O
Δ 4 hr
2. KPF6
Jain, A.; Wyland, K. Inorg. Chem Acta.