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SOFT X-RAY SPECTROSCOPY OF BIOORGANIC MATERIALS WITH 3 rd GENERATION SYNCHROTRON SOURCES

SOFT X-RAY SPECTROSCOPY OF BIOORGANIC MATERIALS WITH 3 rd GENERATION SYNCHROTRON SOURCES. Yan Zubavichus Kurchatov Centre for Synchrotron Radiation and Nanotechnology. Biologically relevant materials:.

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SOFT X-RAY SPECTROSCOPY OF BIOORGANIC MATERIALS WITH 3 rd GENERATION SYNCHROTRON SOURCES

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

  2. 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 Russian-Italian seminar 11 December 2009

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

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

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

  6. 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 Russian-Italian seminar 11 December 2009

  7. a b 4 3 5 2 1 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) Preparation: Molecular Beam deposition with a Knudsen effusion cell Surface chemistry of ultrathin films of histidine on gold as probed by high-resolution synchrotron XPS Y. Zubavichus et al. JPCB109 (2005) 884 Russian-Italian seminar 11 December 2009

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

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

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

  11. C,N,O NEXAFS library fornative amino acids Sample preparation: “as is” powders pressed into In foil NEXAFS data acquisition in the partial electron yield mode Innershell Absorption Spectroscopy of Amino Acids at All Relevant Absorption Edges, Y. Zubavichus, et al. J. Phys. Chem. A109 (2005) 6998. Russian-Italian seminar 11 December 2009

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

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

  14. 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., NIMA603(2009), 111 Russian-Italian seminar 11 December 2009

  15. Amino acids  peptides: NEXAFS fingerprints of the peptide bonds glycine diglycine tryglycine 2,5-diketopiperazine DKP(glycine anhydride – cyclic dipeptide) NEXAFS study of glycine and glycine-based oligopeptides, Y. Zubavichus, et al. J. Electr. Spectr. Relat. Phenom.134 (2004) 25 Russian-Italian seminar 11 December 2009

  16. One more step ahead: homopolypeptides (designed polymers composed of one sort of amino acids) [ ] [ ] [ ] Polytyrosine Polyhistidine Polyisoleucine NEXAFS spectroscopy of homopolypeptides at allrelevant absorption edges: polyisoleucine,polytyrosine, and polyhistidine, Y. Zubavichus, et al.,J. Phys. Chem. B, (2007) 111 9803 Russian-Italian seminar 11 December 2009

  17. Towards functional proteins Collagen (300 kDa) BSA (66 kDa) Lysozyme (14.4 kDa) Fractions of amino acid residues Is X-ray absorption spectroscopy sensitive to the amino acid composition offunctional proteins?, Y.Zubavichus, et al.,J. Phys. Chem. B112 (2008) 4478. Russian-Italian seminar 11 December 2009

  18. 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. B112(44) (2008) 13711-13716. Russian-Italian seminar 11 December 2009

  19. Soft X-ray spectroscopic studies of solutions: 2 approaches Microfluidicliquid cellwith a thin window semi-transparent to soft X-rays Microjet of a solution + efficient differential pumping Window material: Si3N4, SiC (50-100 nm) 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., NIMA585 (2008) 172 Only photon in – photon out techniques (XES, FlY NEXAFS, RIXS) All techniques are available Russian-Italian seminar 11 December 2009

  20. Full O1s RIXS map of liquid water Si3N4 Membrane (75 nm) Two states : -Н-bonded intact water molecules -Ultrafast proton transfer induced by the oxygen core hole Isotope and Temperature Effects in Liquid Water Probed by X-Ray Absorption and Resonant X-Ray Emission Spectroscopy, O. Fuchs et al., PRL100 (2008) 027801 & 249802 Russian-Italian seminar 11 December 2009

  21. NEXAFS XES NH3+NH2 Aqueous glycine: pH effects SiC Membrane (75 nm) N K-edge NEXAFS N K XES Soft x-ray spectroscopy of organic molecules and liquids, O. Fuchs PhD thesis (2009) Russian-Italian seminar 11 December 2009

  22. 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 Russian-Italian seminar 11 December 2009

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

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