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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)2Amber Harding1, Allen G. Oliver2, Jeanette Krause3, Kaitlyn Wyland1,Avijita Jain1 and Charles H. Lake1

1Department of Chemistry, Indiana University of Pennsylvania, Indiana, PA 157052 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 crystalscrystallized in the triclinic crystal system P11,213 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

NN

N

N

N

N

hνRu

NN

N

N

solvent

solvent

DNA Ru

NN

N

N

DNA

Ru

NN

N

N

N

N

hνRu

NN

N

N

solvent

solvent

DNA Ru

NN

N

N

DNA

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 collectedby 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

P

[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

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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 plotshowing 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 ÅTilt = 5.10

3.661 ÅTilt = 9.10

3.801 ÅTilt = 5.00

3.661 ÅTilt = 9.10

3.715 ÅTilt = 25.70

3.487 ÅTilt = 25.60

3.800 ÅTilt = 31.00

3.638 ÅTilt = 8.20

3.965 ÅTilt = 0.00

3.638 ÅTilt = 7.90RuCl3 x H2O + 2 DMF

Δ 1 hr

+1. EtOH +H2O

Δ 4 hr2. KPF6

Jain, A.; Wyland, K. Inorg. Chem Acta.