A study of the feasibility of single molecule scattering analysis with X-ray free electron lasers

Kyungtae Kim; Heesoo Kim; Tai-Hee Kang; Moonhor Ree

Macromolecular Research, Vol.22, No.1, 8-18, January, 2014

DOI10.1007/s13233-014-2015-z Export Citation

A study of the feasibility of single molecule scattering analysis with X-ray free electron lasers

Kyungtae Kim¹, Heesoo Kim^{2, †}, Tai-Hee Kang³, and Moonhor Ree^{1, 3, †}

¹Department of Chemistry, Division of Advanced Materials Science, Center for Electro-Photo Behaviors in Advanced Molecular Systems, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science and Technology, Gyeongbuk, 790-784, Korea
²Department of Microbiology, Dongguk University College of Medicine, Gyeongbuk, 780-714, Korea
³Pohang Accelerator Laboratory, Pohang University of Science and Technology, Gyeongbuk, 790-784, Korea

E-mail:,

The feasibility of single molecule elastic scattering analysis with the X-ray free electron laser (XFEL) sources in operation and under construction around the world was investigated for various biological and synthetic materials (pepsin, polyethylene, poly(4,4′-oxydiphenylene pyromellitimide), and ferric oxide). It was found that existing XFEL facilities provide coherent pulse X-ray beams with the required energies (8.3-12.4 keV), but their fluxes are too low for single molecule elastic scattering experiment to determine the three-dimensional structures of such molecules. For single molecule scattering, the XFEL facilities need to improve their beam flux density to 2×1015 to 7×1018 photons pulse^(-1) μm^(-2), depending on the beam energy. However, the existing XFEL facilities’ sources were found to enable the elastic scattering analysis of pepsin and synthetic polymers with sample sizes of 1-160 μm, as well as of ferric oxide with sample sizes of ≥80 nm. These criteria for the sample size can be extended to other soft (biological, organic, and polymer molecules) and hard (molecules containing heavy metals) materials. In addition, the inelastic scattering, absorption, and radiation damage characteristics of the chosen materials when exposed to the XFEL sources were examined.

Keywords:X-ray free electron laser;single molecule scattering;elastic scattering;inelastic scattering;absorption

[References]

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[1] Madey JJM, J. Appl. Phys., 42, 1906 (1971)

[2] Bonifacio R, Pellegrini C, Narducci LM, Opt. Commun., 50, 373 (1984)

[3] Kim KJ, Phys. Rev. Lett., 57, 1871 (1986)

[4] Ayvazyan V, Baboi N, Bahr J, Balandin V, Beutner B, Brandt A, Bohnet I, Eur. Phys. J. D, 37, 297 (2006)

[5] Feldhaus J, J. Phys. B: At. Mol. Opt. Phys., 43, 194002 (2010)

[6] Emma P, Akre R, Arthur J, Bionta R, Bostedt C, Bozek J, Brachmann A, Bucksbaum P, Coffee R, Decker FJ, Ding Y, Dowell D, Edstrom S, Fisher A, Frisch, Gilevich S, Hastings J, Hays G, Hering P, Huang Z, Iverson R, Loos H, Messerschmidt M, Miahnahri A, Moell, Nat. Photonics, 4, 641 (2010)

[7] Pile D, Nat. Photonics, 5, 456 (2011)

[8] Ishikawa T, Aoyagi H, Asaka T, Asano Y, Azumi N, Bizen T, Ego H, Fukami K, Fukui T, Furukawa Y, Goto S, Hanaki H, Hara T, Hasegawa T, Hatsui T, Higashiya A, Hirono T, Hosoda N, Ishii M, Inagaki T, Inubushi Y, Itoga T, Joti Y, Nat. Photonics, 6, 540 (2012)

[9] Huang Z, Lindau I, Nat. Photonics, 6, 505 (2012)

[10] Schneidmiller EA, Yurkov MV, Eds., Photon Beam Properties at the European XFEL, Deutsches Elektronen-Synchrotron (DESY), Hamburg, 2011.

[11] Ree M (Director (2007.2011) of Pohang Accelerator Laboratory (PAL)) and XFEL Team succeeded to launch the Pohang Accelerator Laboratory X-Ray Free Electron Laser (PAL-XFEL) project (426 M$/2011.2014) as a Korea government project (this project was approved in 2010 and the XFEL construction was started in January, 2011).

[12] PAL X-Ray Free Electron Laser Facility Technical Design Report, Pohang Accelerator Laboratory, Pohang, 2010.

[13] Ganter R, Ed., SwissFel Conceptual Design Report, Paul Scherrer Institut, Villigen, 2010.

[14] Ackermann W, Asova G, Ayvazyan V, Azima A, Baboi N, Bahr J, Balandin V, Beutner B, Brandt A, Bolzmann A, Brinkmann R, Brovko OI, Castellano M, Castro P, Catani L, Chiadroni E, Choroba S, Cianchi A, Costello JT, Nat. Photonics, 1, 336 (2007)

[15] Shintake T, Tanaka H, Hara T, Tanaka T, Togawa K, Yabashi M, Otake Y, Asano Y, Bizen T, Fukui T, Goto S, Higashiya A, Hirono T, Hosoda N, Inagaki T, Nat. Photonics, 2, 555 (2008)

[16] Ullrich J, Rudenko A, Moshammer R, Annu. Rev. Phys. Chem., 63, 635 (2012)

[17] Yefanov OM, Zozulya AV, Vartanyants IA, Stangl J, Mocuta C, Metzger TH, Bauer G, Boeck T, Schmidbauer M, Appl. Phys. Lett., 94, 123104 (2009)

[18] Neutze R, Wouts R, van der Spoel D, Weckert E, Hajdu J, Nature, 406, 752 (2000)

[19] Miao J, Chapman HN, Kirz J, Sayre D, Hodgson KO, Annu. Rev. Biophys. Biomol. Struct., 33, 157 (2004)

[20] Shintake T, Phys. Rev. E, 78, 041906 (2008)

[21] Vartanyants IA, Singer A, New J. Phys., 12, 035004 (2010)

[22] Fratalocchi A, Ruocco G, Phys. Rev. Lett., 106, 105504 (2011)

[23] Caleman C, Huldt G, Maia FRNC, Ortiz C, Parak FG, Hajdu J, van der Spoel D, Chapman HN, Timneanu N, ACS Nano, 5, 139 (2011)

[24] Paithankar KS, Garman EF, Acta Crystallogr., D66, 381 (2010)

[25] Kai T, Phys. Rev., A, 81, 023201 (2010)

[26] Yabashi M, Ishikawa T, Eds., XFEL/SPring-8 Beamline Technical Design Report Ver. 2.0, Experimental Facility Group, RIKEN JASRI XFEL Project Head Office, Hyogo, 2010.

[27] Jin KS, Rho Y, Kim J, Kim H, Kim IJ, Ree M, J. Phys. Chem. B, 112(49), 15821 (2008)

[28] Men YF, Rieger J, Lindner P, Enderle HF, Lilge D, Kristen MO, Mihan S, Jiang SC, J. Phys. Chem. B, 109(35), 16650 (2005)

[29] Song HH, Wu DQ, Ree M, Stein RS, Phillips JC, LeGrand A, Chu B, Macromolecules, 21, 1180 (1988)

[30] Ree M, Nunes TL, Lin JS, Polymer, 35(6), 1148 (1994)

[31] Ree M, Kim K, Woo SH, Chang H, J. Appl. Phys., 81, 698 (1997)

[32] Ree M, Macromol. Res., 14(1), 1 (2006)

[33] Shin TJ, Lee B, Youn HS, Lee KB, Ree M, Langmuir, 17(25), 7842 (2001)

[34] Shin TJ, Ree M, J. Phys. Chem. B, 111(50), 13894 (2007)

[35] Pauling L, Hendricks SB, J. Am. Chem. Soc., 47, 781 (1925)

[36] Blake RL, Hessevick RE, Zoltai T, Finger LW, Am. Miner., 51, 123 (1966)

[37] Howells MR, Beetz T, Chapman HN, Cui C, Holton JM, Jacobsen CJ, Kirz J, Lima E, Marchesini S, Miao H, Sayre D, Shapiro DA, Spence JCH, Starodub D, J. Electron Spectros. Relat. Phenomena, 170, 4 (2009)

[38] Thompson AC, Ed., in X-Ray Data Booklet, 3rd ed., Lawrence Berkeley National Laboratory, University of California, Berkeley, 2009, pp 1-38.

[39] Hubbell JH, Veigele WJ, Bringgs EA, Brown RT, Cromer DT, Howerton RJ, J. Chem. Ref. Data, 4, 471 (1975)

[40] Henke BL, Gullikson EM, Davis JC, Atom. Data Nucl. Data Tables, 54, 181 (1993)

[41] Huldt G, Szoke A, Hajdu J, J. Struct. Biol., 144(1-2), 219 (2003)

[42] Henderson R, Proc. R. Soc. London B, 241, 6 (1990)