Abstract
The intensity of single X-ray pulses from third generation synchrotrons like the ESRF, APS and Spring8 is now so high that it is feasible to conduct time resolved experiment with diffraction, scattering and spectroscopic techniques on samples ranging from small molecules to proteins, with 100 ps time resolution. This limit is dictated by the X-ray pulse length from a synchrotron. In a time-resolved X-ray experiment one first needs to initiate the process of interest in the sample and then open the X-ray shutter and record the signal as a function of time. In the experiments shown in this review, the signals are recorded on a large CCD detector in order to record the signal efficiently in space. Unfortunately, the time-resolution of current CCDs is still too slow, 100 μs at best, to be useful for monitoring molecular processes on molecular time scales. The only way to explore faster phenomena is to use the pump-probe method where the time resolution is obtained from varying the pump-probe delay. In the examples discussed here, the samples were excited by picosecond or nanosecond laser pulses and the excited samples were probed by 100 ps X-ray pulses from an undulator.
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References
Schotte F, Techert S, Anfinrud PA, Srajer V, Moffat K, Wulff M (2002) Picosecond structural studies using pulsed synchrotron radiation. In: Dennis M (ed) Third-generation hard X-ray synchrotron radiation sources. Wiley, New York, pp 345–401. ISBN 0-471-31433-1
Wulff M, Plech A, Eybert L, Randler R, Schotte F, Anfinrud P (2002) Realisation of sub-nanosecond pump and probe experiments at the ESRF. Faraday Discuss 122:13–26
Guerin L, Kong Q, Khakhulin D, Cammarata M, Ihee H, Wulff M (2012) Tracking atomic positions in molecular reactions by picosecond X-ray scattering at the ESRF. Synchrotron Radiat News 25(2):25–31
Graber T, Anderson S, Brewer H, Chen Y-S, Cho HS, Dashdorj N, Henning RW, Kosheleva I, Macha G, Meron M, Pahl R, Ren Z, Ruan S, Schotte F, Srajer V, Viccaro PJ, Westferro F, Anfinrud P, Moffat K (2011) BioCARS: a synchrotron resource for time-resolved X-ray science. J Synchrotron Rad 18:658–670
Nozawa S, Adachi S-i, Takahashi J-i, Ryoko Tazaki L, Guerin MD, Tomita A, Sato T, Chollet M, Collet E, Cailleau H, Yamamoto S, Tsuchiya K, Shioya T, Sasaki H, Mori T, Ichiyanagi K, Sawa H, Kawata H, Koshihara S-y (2007) Developing 100 ps-resolved X-ray structural analysis capabilities on beamline NW14A at the photon factory advanced ring. J Synchrotron Rad 14:313–319
Wrobel R, Brullot B, Dainciart F, Doublier J, Eloy J-F, Marmoret R, Vilette B, Mathon O, Tucoulou R, Freund A (1998) Characterisation of ultrafast X-ray detectors at the European Synchrotron Radiation Facility. SPIE 3451:156–161
Ihee H, Lorenc M, Kim TK, Kong QY, Cammarata M, Lee JH, Bratos S, Wulff M (2005) Ultrafast X-ray diffraction of transient molecular structures in solution. Science 309:1223–1227
Kim TK, Lorenc M, Lee JH, Russo M, Kim J, Cammarata M, Kong QY, Noel S, Plech A, Wulff M, Ihee H (2006) Spatiotemporal reaction kinetics probed by picosecond X-ray diffraction. Proc Natl Acad Sci U S A 103:9410–9415
Kong Q, Wulff M, Lee JH, Bratos S, Ihee H (2007) Photochemical reaction pathways of carbon tetrabromide in solution probed by picosecond X-ray diffraction. J Am Chem Soc 129:13584–13591
Lee JH, Kim J, Cammarata M, Kong Q, Kim KH, Choi J, Kim TK, Wulff M, Ihee H (2008) Transient X-ray diffraction reveals global and major reaction pathways for the photolysis of iodoform in solution. Angew Chem Int Ed 47:1047–1050
Lee JH, Kim TK, Kim J, Kong Q, Cammarata M, Lorenc M, Wulff M, Ihee H (2008) Capturing transient structures in the elimination reaction of haloalkane in solution by transient X-ray diffraction. J Am Chem Soc 130:5834–5835
Plech A, Wulff M, Bratos S, Mirloup F, Vuilleumier R, Schotte F, Anfinrud PA (2004) Visualizing chemical reactions in solution by picosecond x-ray diffraction. Phys Rev Lett 92:125505
Wulff M, Bratos S, Plech A, Vuilleumier R, Mirloup F, Lorenc M, Kong Q, Ihee H (2006) Recombination of photodissociated iodine: a time-resolved x-ray diffraction study. J Chem Phys 124:034501
Cammarata M, Lorenc M, Kim TK, Lee JH, Kong QY, Pontecorvo E, Lo Russo M, Schiro G, Cupane A, Wulff M, Ihee H (2006) Impulsive solvent heating probed by picosecond X-ray diffraction. J Chem Phys 124:124504
Kong QY, Lee JH, Plech A, Wulff M, Ihee H, Koch MHJ (2008) Ultrafast X-ray solution scattering reveals an unknown reaction intermediate in the photolysis of Ru3(CO)12. Angew Chem Int Ed 47:5550–5553
Plech A, Kotaidis V, Lorenc M, Wulff M (2005) Thermal dynamics in laser excited metal nanoparticles. Chem Phys Lett 401:565–569
Cammarata M, Levantino M, Schotte F, Anfinrud PA, Bowman RM, Gruebele M, Zewail AH, Ewald F, Choi J, Cupane A, Wulff M, Ihee H (2008) Tracking the structural dynamics of proteins in solution using time-resolved wide-angle scattering. Nat Methods 5:881–887
Cho HS, Dashdorj N, Schotte F, Graber T, Henning R, Anfinrud P (2010) Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering. Proc Natl Acad Sci U S A 107(16):7281–7286
Baumert T, Pederson S, Zewail AH (1993) Femtosecond real-time probing of reactions. Vectorial dynamics of transition states. J Phys Chem 97:12447–12459
Dantus M, Bowman RM, Gruebele M, Zewail AH (1989) Femtosecond real-time probing of reactions: the reaction of IHgI. J Chem Phys 91:7437–7450
Zhong D, Zewail AH (1998) Femtosecond real-time probing of dynamics and structure in charge-transfer reactions. J Phys Chem A 102:4031–4058
Pugliano N, Szarka AZ, Gnanakaran S, Triechel M, Hochstrasser RM (1995) Vibrational population-dynamics of the HgI photofragment in ethanol solution. J Chem Phys 103:6498–6511
Pugliano N, Szarka AZ, Hochstrasser RM (1996) Relaxation of the product state coherence generated through the photolysis of HgI2 in solution. J Chem Phys 104:5062–5079
Volk M, Gnanakaran S, Gooding E, Kholodenko Y, Pugliano N, Hochstrasser RM (1997) Anisotropy measurements of solvated HgI2 dissociation: transition state and fragment rotational dynamics. J Phys Chem A 101:638–643
The values for rate coefficients and time constants are corrected by a factor of 2 with respect to the published values due to a simple error of doubling the rate constant in the global-fitting program for TRXL data
Fossey J, Lefort D, Sorba J (1995) Free radicals in organic chemistry. Wiley, New York
Ihee H, Kua J, Goddard WA, Zewail AH (2001) CF2XCF2X and CF2XCF2 center dot radicals (X = Cl, Br, I): Ab initio and DFT studies and comparison with experiments. J Phys Chem A 105:3623–3632
Ihee H, Zewail AH, Goddard WA (1999) Conformations and barriers of haloethyl radicals (CH2XCH2, X = F, Cl, Br, I): Ab initio studies. J Phys Chem A 103:6638–6649
Skell PS, Tuleen DL, Readio PD (1963) Stereochemical evidence of bridged radicals. J Am Chem Soc 85:2849–2850
Ihee H, Lobastov VA, Gomez UM, Goodson BM, Srinivasan R, Ruan CY, Zewail AH (2001) Direct imaging of transient molecular structures with ultrafast diffraction. Science 291:458–462
Ihee H, Goodson BM, Srinivasan R, Lobastov VA, Zewail AH (2002) Ultrafast electron diffraction and structural dynamics: transient intermediates in the elimination reaction of C2F4I2. J Phys Chem A 106:4087–4103
Lee JH, Wulff M, Bratos S, Petersen J, Guerin L, Leicknam J-C, Cammarata M, Kong Kim Q, Møller KB, Ihee H (2013) Filming the birth of molecules and accompanying solvent rearrangement. J Am Chem Soc 135:3255–3261
Srajer V, Teng T, Ursby T, Pradervand C, Ren Z, Adachi S, Schildkamp W, Bourgeois D, Wulff M, Moffat K (1996) Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography. Science 274:1726–1729
Schotte F, Lim M, Jackson TA, Smirnov A, Soman J, Olson JS, Phillips GN, Wulff M, Anfinrud PA (2003) Watching a protein as it functions with 150-ps time-resolved X-ray crystallography. Science 300:1944–1947
Schotte F, Cho HS, Soman J, Wulff M, Olson JS, Anfinrud P (2013) Real-time tracking of CO migration and binding in the alpha and beta subunits of human hemoglobin via 150-ps time-resolved Laue crystallography. Chem Phys D-12:00661R1
Perman B, Srajer V, Ren Z, Teng T-Y, Pradervand C, Ursby T, Schotte F, Wulff M, Kort R, Hellingwerf K, Moffat K (1998) Energy transduction on the nanosecond time scale: early structural events in a xanthopsin photocycle. Science 279:1946–1950
Schotte F, Cho HS, Kail Ville RI, Kamikubo H, Dashdorja N, Henry ER, Graber TJ, Henning R, Wulff M, Hummer G, Kataoka M, Anfinrud PA (2012) Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proc Natl Acad Sci U S A 109(47):19256–19261
Jung YO, Lee JH, Kim J, Schidt M, Moffat K, Srajer V, Ihee H (2013) Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography. Nat Chem 5(3):212–220
Wöhri AB, Katona G, Johansson LC, Fritz E, Malmerberg E, Andersson M, Vincent J, Eklund M, Cammarata M, Wulff M, Davidsson J, Groenhof G, Neutze R (2010) Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction. Science 328(5978):630–633
Lim M, Jackson TA, Anfinrud PA (1995) Binding of CO to myoglobin from a hemepocket docking site to form nearly linear Fe-C-O. Science 269:962
Lim M, Jackson TA, Anfinrud PA (1997) Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin. Nat Struct Biol 4:209
Chu K, Vojtchovsky J, McMahon BH, Sweet RM, Berendzen J, Schlichting I (2000) Structure of a ligand-binding intermediate in wild-type carbonmonooxy myoglobin. Nature 403:921
Ostermann A, Waschipky R, Parak FG, Nienhaus GU (2000) Ligand binding and conformational motions in myoglobin. Nature 404(6774):205–208
Srajer V, Ren Z, Teng TY, Schmidt M, Ursby T, Bourgeois D, Pradervand C, Schildkamp W, Wulff M, Moffat K (2001) Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction. Biochemistry 40:13802
Nibbering ETJ, Fidder H, Pines E (2005) Ultrafast chemistry: using time-resolved vibrational spectroscopy for interrogation of structural dynamics. Annu Rev Phys Chem 56:337–367
Kukura P, McCamant DW, Mathies RA (2007) Femtosecond stimulated Raman spectroscopy. Annu Rev Phys Chem 58:461–488
Hamm P, Lim MH, Hochstrasser RM (1998) Structure of the amide I band of peptides measured by femtosecond nonlinear-infrared spectroscopy. J Phys Chem B 102:6123–6138
Zheng J, Kwak K, Fayer MD (2007) Ultrafast 2D IR vibrational echo spectroscopy. Acc Chem Res 40:75–83
Bressler C, Chergui M (2004) Ultrafast X-ray absorption spectroscopy. Chem Rev 104:1781–1812
Khalil M, Marcus MA, Smeigh AL, McCusker JK, Chong HHW, Schoenlein RW (2006) Picosecond x-ray absorption spectroscopy of a photoinduced iron(II) spin crossover reaction in solution. J Phys Chem A 110:38–44
Gawelda W, Johnson M, de Groot FMF, Abela R, Bressler C, Chergui M (2006) Electronic and molecular structure of photoexcited [Ru-II(bpy)(3)](2+) probed by picosecond X-ray absorption spectroscopy. J Am Chem Soc 128:5001–5009
Pham VT, Gawelda W, Zaushitsyn Y, Kaiser M, Grolimund D, Johnson SL, Abela R, Bressler C, Chergui M (2007) Observation of the solvent shell reorganization around photoexcited atomic solutes by picosecond X-ray absorption spectroscopy. J Am Chem Soc 129:1530–1531
Gawelda W, Pham VT, Benfatto M, Zaushitsyn Y, Kaiser M, Grolimund D, Johnson SL, Abela R, Hauser A, Bressler C, Chergui M (2007) Structural determination of a short-lived excited iron(II) complex by picosecond x-ray absorption spectroscopy. Phys Rev Lett 98:057401
Chen LX, Jager WJH, Jennings G, Gosztola DJ, Munkholm A, Hessler JP (2001) Capturing a photoexcited molecular structure through time-domain X-ray absorption fine structure. Science 292:262–264
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Wulff, M. et al. (2014). Molecular Dynamics Probed by Short X-ray Pulses from a Synchrotron. In: Howard, J., Sparkes, H., Raithby, P., Churakov, A. (eds) The Future of Dynamic Structural Science. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-8550-1_19
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DOI: https://doi.org/10.1007/978-94-017-8550-1_19
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