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Determining the Structure of Platinum Streptidine using X-Ray Absorption Spectroscopy. Micha ë lle Mayalu Massachusetts Institute of Technology SULI Program: Stanford Synchrotron Radiation Laboratory, SLAC Mentor: Serena DeBeer George August, 15, 2007. Outline. Platinum Anti-Cancer Agents - PowerPoint PPT Presentation
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Determining the Structure of Platinum Streptidine using X-Ray Absorption
Spectroscopy
Michaëlle Mayalu
Massachusetts Institute of Technology
SULI Program: Stanford Synchrotron Radiation Laboratory, SLAC
Mentor: Serena DeBeer George
August, 15, 2007
Outline
Platinum Anti-Cancer Agents X-Ray Absorption Spectroscopy Data Analysis Conclusion
Platinum Anti-Cancer Agents
•Background•Platinum Streptidine
Background
Platinum complexes have been discovered to stop cell division
This has useful applications in treating cancer and considerable advances have been made
However…..
mechanisms are that lead to the drug being taken up by the cell membrane and integrated into the DNA are still unknown
the drug is successful in treating some types of cancers but ineffectual treating other types
platinum drugs such as cisplatin has been found to be very toxic causing nephrotoxity, neuropathy, ototoxicity, hematological toxicity, neuropathology and seizures.
Consequently, the search for improved platinum drugs that treat a wider range of cancers and display fewer toxic side effects still continues.
Platinum Streptidine Because the structure and
coordination of the drug (especially in solution) is essential to understanding how the drug interacts with molecules in the body, X-ray absorption spectroscopy (XAS) is a powerful tool for determining the local structure of this newly developed drug.
main questions to hopefully be answered by analysis of XAS data measured with XAS are: 1. Is it the Pt coordinated to the
Streptidine? 2. And if this is the case through which
atoms
Putative structures (obtained from elemental analysis and nuclear magnetic resonance)
OH7
NH13
NH14H14N
OH8
H9ONH10
H11N
NH11
H12O
H1
H2
H3
H4
H5
H6
•Streptidine
OHNH
NHH2N
OH
ONHN
NH2
HO
PtCl S
OHNH
NHH2N
OH
ON
HO
HN
NHPt
S
OHNH
NHHN
OH
HONH
HOHN
HN
PtCl
S
1 2 3
OH
NHNH
H2N
OHHO
NH HOHN
H2N Pt
ClS
N. Aliaga-Alcalde and Jan Reedijk
X-Ray Absorption Spectroscopy
•What Is It •Measurements•Applications
What is it?
h
continuum
Emitted photo-electron
1s
Auger electron
2p
2s
X-ray FluorescenceX-ray FluorescenceDirect AbsorptionDirect Absorption(Transmittance)(Transmittance)
hfluorescent photon
George DeBeer, S.
What is it?
Pt-L3 Edge 11550 eV
www.chem.ucalgary/groups/farideh/xas.pdf
Measurements
X-ray Source
Monoslits
Double Crystal
Monochromator
Ta Slits
I0
Sample
Detector
I1
Foil
I2
Experimental Hutch
George DeBeer, S.
Measurements: Transmittance When a beam of monochromatic X-rays goes through matter, it loses its intensity due to interaction with the atoms in the material. The intensity drops exponentially with distance if the material is homogeneous, and after transmission the intensity
is:
I0=Ie-μt
Where:
I incident X-ray intensity I0 transmitted X-ray intensity µ absorption coefficient t is the thickness of the sample
Absorption can therefore be measured as:
A= µt=ln(I0/I)
www.ssrl.slac.stanford.edu/dichroism/xas
Transmittance
I0 ISample
X-rays
Ion chamber Ion chamber
A = μt = ln (I0/I1)
μ ,absorption coefficientt sample thickness
t
+
-Ionizing radiation (i.e. X-rays) creates ion pairs in the gas and the sweeping voltage results in a current flow.
X-rays
George DeBeer, S.
Measurements: Fluorescence
Fluorescence detector
sample
X-ray
Soller Slits
filter
George DeBeer, S.
X-Ray Absorption Spectrum (edge + EXAFS)
Pre-edgeand Edge(XANES)
EXAFS (extended x-ray absorption fine structure)
XAS or XAFS
Energy
Abs
orpt
ion
Coe
ffici
ent (
mu)
Applications
George DeBeer, S.
constructive interferenceresults in a maximum
destructive interferenceresults in a minimum
Applications
Extended X-Ray absorption fine structure
George DeBeer, S.
Data Analysis
Processing Data
Analyzing Results
Fitting Data
eV
1.4
Pre-edge subtraction: A procedure performed to subtract the total absorption from the absorption of the edge in interest.
0.4
0.6
0.8
1.0
1.2
6800 7000 7200 7400 7600 7800 8000
Raw
Spline: A method for removing the atomic background from the absorption curve (i.e. the absorption due to the photoabsorber alone, with out any neighboring atoms) .
eV
0.0
0.5
1.0
1.5
6800 7000 7200 7400 7600 7800 8000
Nor
ma
l
Raw data: This is the way that the XAS transmission mode spectrum looks, right off the beam line.
0.4
0.6
0.8
1.0
1.2
1.4
6800 7000 7200 7400 7600 7800 8000
Raw
Getting the EXAFS
Processing Data
George DeBeer, S.
Processing Data
-6
-4
-2
0
2
4
6
4 6 8 10 12(Å-1)k
EX
AF
S*k
3
4 6 8 10 12(Å-1)k
EX
AF
S*k
3 Cu-N
Cu-S
data + fit
Cu-C2/C5 (SS)
Cu-N-C2/C5 (MS)
Cu-C3/N4 (SS)
Cu-N-C3/N4 (MS)
EXAFS data is really a sum of sine waves. The goal of fitting data is to deconvolute the total signal into its components.
A Fourier transformallows you tovisualize the radialdistribution of atoms.
Note:
k is the photoelectron wave number.
k= (2m(E-E0)/ћ2)1/2
EXAFS data are k-weighted to enhance oscillations at high-k.
Getting Information from EXAFS Data
George DeBeer, S.
0.0
5.0
10.0
15.0
0 1 2 3 4 5 6
FT
Mag
nitu
de
R (Å)
Analyzing Results
Pt-Std Edges Solid and Solution
As can be seen, the edges of the solid and solution data begin at different energies
Because the solid begins at a lower energy, it is more reduced
This suggests that the solid structure is surrounded by heavier atoms
solid
soln
-2.00E-01
0.00E+00
2.00E-01
4.00E-01
6.00E-01
8.00E-01
1.00E+00
1.20E+00
1.40E+00
1.60E+00
11540 11545 11550 11555 11560 11565 11570 11575 11580
Energy(eV)
Ab
sorb
ance
Analyzing Results
-8.00E+00
-6.00E+00
-4.00E+00
-2.00E+00
0.00E+00
2.00E+00
4.00E+00
6.00E+00
8.00E+00
1.00E+01
Energy(eV)
X(k
)*k^
3
0.00E+00
5.00E-01
1.00E+00
1.50E+00
2.00E+00
2.50E+00
0.00E+00 1.00E+00 2.00E+00 3.00E+00 4.00E+00 5.00E+00 6.00E+00 7.00E+00 8.00E+00
R(A)
Tra
nsf
orm
Mag
nit
ide
K3 EXAFS and Corresponding Fourier Transforms
amplitude of the EXAFS slightly decreases from solid to soln
this indicate a decrease in coordination number or may also be indicative of lighter atoms present in solution.
intensity of FT greatly decreases from solid to solution.
Similar to the decrease in EXAFS amplitude, the decrease in peak intensity indicates a decrease in coordination or lighter atoms ligated to the Platinum in solution.
Fitting DataInitial Model
Calculation of initial distance & disorder
parameters.
Optimization of distance & disorder
parameters.
Are fit parameters reasonable & is fit
quality good?
Compare with other good fits to determine
best fit.
YesNo
George DeBeer, S.
-10
-8
-6
-4
-2
0
2
4
6
8
10
0 2 4 6 8 10 12 14 16
k(A^-1)
EX
AF
S*k
^3
EXAFS
FIT
Solid Pt-Std 4 Pt-Cl at 2.30 Å Normalized error
0.567 F/(No. pts)
Best Fit: 4 Pt-Cl at 2.30 Å and 1 Pt-N at 2.02 Å
Comparison of K2PtCl4 and C8H18N6O7Cl4Pt
-2.00E-01
0.00E+00
2.00E-01
4.00E-01
6.00E-01
8.00E-01
1.00E+00
1.20E+00
1.40E+00
1.60E+00
11540 11545 11550 11555 11560 11565 11570 11575 11580
Energy(eV)
Ab
sorb
ance
Pt
Cl Cl
Cl ClN
Normalized error: 0.547F/(No. pts)
-10
-8
-6
-4
-2
0
2
4
6
8
10
0 2 4 6 8 10 12 14 16
k(A^-1)
EX
AF
S*k
^3
EXAFS
FIT
0.00E+00
5.00E-01
1.00E+00
1.50E+00
2.00E+00
2.50E+00
3.00E+00
0.00E+00 5.00E-01 1.00E+00 1.50E+00 2.00E+00 2.50E+00 3.00E+00 3.50E+00 4.00E+00
R(A)
FT
Mag
nit
ud
e
FT
FT FIT
0.00E+00
5.00E-01
1.00E+00
1.50E+00
2.00E+00
2.50E+00
3.00E+00
0.00E+00 5.00E-01 1.00E+00 1.50E+00 2.00E+00 2.50E+00 3.00E+00 3.50E+00 4.00E+00
R(A)
FT
Ma
gn
itu
de
FT
FT FIT
Solution Pt-Std
-6
-4
-2
0
2
4
6
8
0 2 4 6 8 10 12 14
k(A^-1))
EX
AF
S*k
^3
EXAFS
FIT
4 Pt-Cl/S at 2.30 Å 1 Pt-N at 2.03 Å
Normalized error: 0.359F/(No. pts)
0.00E+00
2.00E-01
4.00E-01
6.00E-01
8.00E-01
1.00E+00
1.20E+00
1.40E+00
1.60E+00
1.80E+00
0.00E+00 5.00E-01 1.00E+00 1.50E+00 2.00E+00 2.50E+00 3.00E+00 3.50E+00 4.00E+00
R(A)
FT
Mag
nit
ud
e
FT
FT FIT
-6
-4
-2
0
2
4
6
8
0 2 4 6 8 10 12 14
k(A^-1)
EX
AF
S*k
^3
EXAFS
FIT
Solution Pt-Std Best Fit: 3 Pt-Cl/S at 2.30 Å and 2 Pt-N at 2.08 Å
Pt
Cl/S Cl/S
NN
Normalized error: 0.363 F/(No. pts)
0.00E+00
2.00E-01
4.00E-01
6.00E-01
8.00E-01
1.00E+00
1.20E+00
1.40E+00
1.60E+00
1.80E+00
0.00E+00 5.00E-01 1.00E+00 1.50E+00 2.00E+00 2.50E+00 3.00E+00 3.50E+00 4.00E+00
R(A)
FT
Mag
nit
ud
e
FT
FT FIT
Cl/S
Conclusion
Conclusion It can be concluded that Platinum is in fact coordinated to the
streptidine through a bond with nitrogen. In the solid…
the streptidine is coordinated to the Pt by one nitrogen at 2.02 Å
In the solution… the streptidine could be coordinated to 1-2 nitrogens, although
with 2 nitrogens at 2.08 Å is more likely.
This is shown by analysis and fitting of the EXAFS data of the solid and solution Pt-Std and comparing the edges and EXAFS of the Pt-Std solid and solution
Future work should include the determination of how many chlorines and sulfurs are ligated in the solution structure.
Acknowledgments
Special Thanks to:
My Mentor Serena Debeer George U. S. Department of Energy, Office of Science for
giving me the opportunity to participate in the SULI
References Serena DeBeer George, Introduction to Extended X-ray
Absorption Fine Structure (EXAFS) Spectroscopy and its Applications (Power Point)
XAS Short Course for Structural Molecular Biology Applications
www.chem.ucalgary/groups/farideh/xas.pdf
www.ssrl.slac.stanford.edu/dichroism/xas
N. Aliaga-Alcalde and Jan Reedijk, University of Leiden, the Netherlands, unpublished results, Pt-Std (Platinum-Streptidine complexes)