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Russian-Italian seminar 11 December 2009 SOFT X-RAY SPECTROSCOPY OF BIOORGANIC MATERIALS WITH 3 rd GENERATION SYNCHROTRON SOURCES Yan Zubavichus Kurchatov.

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Presentation on theme: "Russian-Italian seminar 11 December 2009 SOFT X-RAY SPECTROSCOPY OF BIOORGANIC MATERIALS WITH 3 rd GENERATION SYNCHROTRON SOURCES Yan Zubavichus Kurchatov."— Presentation transcript:

1 Russian-Italian seminar 11 December 2009 SOFT X-RAY SPECTROSCOPY OF BIOORGANIC MATERIALS WITH 3 rd GENERATION SYNCHROTRON SOURCES Yan Zubavichus Kurchatov Centre for Synchrotron Radiation and Nanotechnology

2 Russian-Italian seminar 11 December 2009 Biologically relevant materials: Small molecules: amino acids, purine and pyrimidine bases, simple carbohydrates, fatty acids, nucleoside phosphates, etc. Macromolecules: proteins, nucleic acids, polysacharides, lipids, etc. Supramolecular complexes: lipoproteins, ribosomes, etc. Organelles: membranes, nuclei, mitochondria, etc. Cells Tissues Biomimicking artificially designed nanostructured materials and devices (sensors, biochips, etc.) Complexity

3 Russian-Italian seminar 11 December 2009 Soft X-ray synchrotron spectroscopy (Photon Energy Range h < 1500 eV)

4 Russian-Italian seminar 11 December 2009 Measurements: - BESSY II, Berlin, Germany (HE- SGM, PM1, UE52 PGM, U41 PGM) - ALS, Berkeley, USA (8.0)

5 Russian-Italian seminar 11 December 2009 Severe experimental problem: Radiation damage Soft X-ray induced decomposition of amino acids: an XPS, mass-spectrometry, and NEXAFS study, Y. Zubavichus, et al., Rad. Res. 161 (2004) 346. Gaseous decomposition products in the residual vacuum Fast changes in PES & NEXAFS spectra

6 Russian-Italian seminar 11 December 2009 Experimental considerations to suppress or avoid damage Light source: BM is easier than undulator Fastest possible data collection Strict control of damage effects by successive scans New series – new spot on a sample (or continuous shift of the sample position during scan) Cooling or efficient heat sink

7 Russian-Italian seminar 11 December 2009 Combined PES + NEXAFS study: Amino acid Histidine (His) on Au(111) Coordinatively active amino acid residue (often responsible for metal- binding in proteins) Exists in a number of charge forms (mediator of electron/proton transfer in proteins) Surface chemistry of ultrathin films of histidine on gold as probed by high-resolution synchrotron XPS Y. Zubavichus et al. JPCB 109 (2005) 884        Preparation: Molecular Beam deposition with a Knudsen effusion cell

8 Russian-Italian seminar 11 December 2009 PES data Film 1: Monolayer Film 2: 3 Molecular layers Film 3: 6 Molecular layers

9 Russian-Italian seminar 11 December 2009 Multilayer film Linear Dichroism in NEXAFS C K-edge N K-edge O K-edge Monolayer film No distinct polarization dependence  no preferred molecular orientation

10 Russian-Italian seminar 11 December 2009 Au Weak van der Waals interactions Strong ionic- covalent bonding Au Multilayer film Monolayer film ZI His His - anions

11 Russian-Italian seminar 11 December 2009 C,N,O NEXAFS library for native amino acids Innershell Absorption Spectroscopy of Amino Acids at All Relevant Absorption Edges, Y. Zubavichus, et al. J. Phys. Chem. A 109 (2005) Sample preparation: “as is” powders pressed into In foil NEXAFS data acquisition in the partial electron yield mode

12 Russian-Italian seminar 11 December 2009 Aspartic acid (Asp) vs. Asparagine (Asn) Phenylalanine (Phe) vs. Tyrosine (Tyr) Amino acids: NEXAFS fingerprints of specific functional groups

13 Russian-Italian seminar 11 December 2009 Effects of the charge state of an amino acid residue in NEXAFS Solid-state NEXAFS spectra of glycine in various charge states, Y. Zubavichus, et al., J. Phys. Chem. B, 110 (2006) 3420 cation neutral molecule zwitter ion anion

14 Russian-Italian seminar 11 December 2009 Amino acids  peptides: compositional effects The ‘building block” approach is valid to a certain extent NEXAFS spectroscopy of biological molecules: from amino acids to functional proteins, Y. Zubavichus, et al., NIMA 603 (2009), 111

15 Russian-Italian seminar 11 December 2009 glycinediglycinetryglycine2,5-diketopiperazine DKP (glycine anhydride – cyclic dipeptide) Amino acids  peptides: NEXAFS fingerprints of the peptide bonds NEXAFS study of glycine and glycine-based oligopeptides, Y. Zubavichus, et al. J. Electr. Spectr. Relat. Phenom. 134 (2004) 25

16 Russian-Italian seminar 11 December 2009 One more step ahead: homopolypeptides (designed polymers composed of one sort of amino acids) [ ] Polyisoleucine Polytyrosine Polyhistidine NEXAFS spectroscopy of homopolypeptides at all relevant absorption edges: polyisoleucine, polytyrosine, and polyhistidine, Y. Zubavichus, et al., J. Phys. Chem. B, (2007)

17 Russian-Italian seminar 11 December 2009 Lysozyme (14.4 kDa) Collagen (300 kDa) BSA (66 kDa) Towards functional proteins Fractions of amino acid residues Is X-ray absorption spectroscopy sensitive to the amino acid composition of functional proteins?, Y.Zubavichus, et al., J. Phys. Chem. B 112 (2008) 4478.

18 Russian-Italian seminar 11 December 2009 C,N,O NEXAFS library for nucleotide bases X-ray absorption spectroscopy of the nucleotide bases at the carbon, nitrogen, and oxygen K-edges, Y. Zubavichus, et al., J. Phys. Chem. B 112(44) (2008)

19 Russian-Italian seminar 11 December 2009 Soft X-ray spectroscopic studies of solutions: 2 approaches Microfluidic liquid cell with a thin window semi- transparent to soft X-rays Window material: Si 3 N 4, SiC ( nm) Microjet of a solution + efficient differential pumping Investigation of volatile liquid surfaces by synchrotron X-ray spectroscopy of liquid microjets, K.R. Wilson, et al., Rev. Sci. Instr. 75 (2004) 725 A liquid flow cell to study the electronic structure of liquids with soft X-rays, O. Fuchs, et al., NIMA 585 (2008) 172 All techniques are available Only photon in – photon out techniques (XES, FlY NEXAFS, RIXS)

20 Russian-Italian seminar 11 December 2009 Full O1s RIXS map of liquid water Si 3 N 4 Membrane (75 nm) Isotope and Temperature Effects in Liquid Water Probed by X-Ray Absorption and Resonant X-Ray Emission Spectroscopy, O. Fuchs et al., PRL 100 (2008) & Two states : -Н-bonded intact water molecules -Ultrafast proton transfer induced by the oxygen core hole

21 Russian-Italian seminar 11 December 2009 Aqueous glycine: pH effects N K-edge NEXAFS N K  XES SiC Membrane (75 nm) Soft x-ray spectroscopy of organic molecules and liquids, O. Fuchs PhD thesis (2009) NH 3 + NH 2 NEXAFSXES

22 Russian-Italian seminar 11 December 2009 Conclusions Synchrotron-based PES, NEXAFS, XES, and RIXS are a highly efficient and informative set of experimental techniques to elucidate organic materials of biological significance in different forms, including bulk powders, thin evaporated films, adsorbates, aqueous solutions, etc. Radiation damage problems are serious but can be avoided The results presented above could be a good starting point for research projects with novel soft X-ray instrumentation at the KCSRNT

23 Russian-Italian seminar 11 December 2009 Acknowledgements University of Heidelberg, Germany University of Würzburg, Germany University of Nevada, Las Vegas, USA University of Graz, Austria Prof. M.Grunze Dr. M.Zharnikov Prof. E. Umbach Dr. O. Fuchs Dr. L. Weinhardt Prof. C. Heske Prof. F. Netzer Dr. G. Tzvetkov


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