Towards Ultrafast Excited State Molecular Structural Studies in Photochemical Processes Using Pulsed X-rays from the Advanced Photon Source

L. X. Chen1, G. B. Shaw1, G. Jennings2, K. Attenkofer2

1 Chemistry Division
2 Experimental Facilities Division, Argonne National Laboratory

Photoexcited molecules are quintessential reactants in photochemistry. Despite their importance in understanding fundamental aspects in photochemistry, structures of these photoexcited molecules in disordered media, (where a majority of photochemical reactions take place) remained elusive for decades due to lack of proper x-ray sources. With new, pulsed x-ray sources now available, short-lived excited-state molecular structures in disordered media can be captured using laser-pulse pump, x-ray-pulse probe techniques at third-generation synchrotrons with time resolutions of 30-100 ps, as demonstrated by examples from our studies at the Advanced Photon Source. These studies provide unprecedented information on structural origins of molecular properties in the excited states. Using other ultrafast x-ray facilities being constructed now and in the near future, time resolution for the excited-state structure measurements could reach the femtosecond regime, which will make molecular movies of bond breaking or formation, as well as vibrational relaxation, a reality.

The work conducted at the Advanced Photon Source was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, U. S. Department of Energy under contract W-31-109-Eng-38.

Search for X-ray Induced Acceleration of the Decay of Isomeric Hafnium

I. Ahmad1, J. C. Banar2, J. A. Becker3, D. S.Gemmell1, A. Mashayekhi4, D. P. McNabb3, E. F. Moore1, R. S.Rundberg2, J. P. Schiffer1, S. D. Shastri4, T. F. Wang3, and J. B. Wilhelmy2

1 Physics Division, Argonne National Laboratory
2 Los Alamos National Laboratory
3 Lawrence Livermore National Laboratory
4 Experimental Facilities Division, Argonne National Laboratory

In 1999 a research team from the University of Texas, Dallas, published a result, which, if correct, would have enormous consequences in several military, industrial, and other applications [1,2]. These researchers, led by Prof. C. B. Collins, found that the natural 31-yr decay of the second isomeric level of the isotope 178Hf (written as 178m2Hf) can be accelerated by about 4% when a target of this material is irradiated with x-rays in the range 20–60 keV from a dental x-ray machine. The 178m2Hf state has an excitation energy of 2.446 MeV above the nuclear ground state. The spin/parity of the state is 16+ and has a quantum number, K = 16 (the projection of the total nuclear spin on the nuclear symmetry axis). 178m2Hf is an example of a so-called K-isomer, many of which are known to exist in this region of the periodic table where highly deformed nuclei are common. The long nuclear half-life of 31 years is primarily due to the inhibiting effect of the large change in nuclear structure required in transitions from the K = 16 isomer to states with much lower K. Almost all of the natural decays of 178m2Hf proceed via lower-lying states in a K = 8 band, in which the band-head is another isomeric state with a half-life of 4 s, and which in turn decays into the K = 0 ground-state band (GSB). The original explanation offered by the Texas group for their observed x-ray “triggering” of the decay of the 16+ isomer is that photons are resonantly absorbed into a “K-mixed” state (or states) lying somewhere in the range 20–60 keV above the isomeric state. Such a state could then decay rapidly via the K-admixture in its wavefunction to a state of lower K and thence promptly to the nuclear ground state. Several researchers pointed out that the experiment and this explanation implied gross violation of well-established sum rules for nuclear photoabsorption.

In 2002, Collins et al. published further results obtained with monochromatic x-ray beams at SPring-8 [1]. Even with these much more intense beams, accelerations of about 2% were observed in the decay of 178m2Hf, but now with x-rays of 9–13 keV. An explanation in terms of “NEET” was proposed.

The Texas results have generated much speculation about γ-ray lasers, “isomer bombs,” “hafnium engines” to power Unmanned Aerial Vehicles, etc. (see, e.g., ref. [2]). To understand the interest in this process, one has only to recall that 1 gram of 178m2Hf (a cube 2 mm on a side) has an energy content equivalent to ~0.3 tons of TNT. This energy would be released in the form of cascade γ-rays.

We have performed two sets of measurements attempting to verify the Texas measurements, using intense white x-ray beams from the APS [3]. Our first set was aimed at the x-ray range 20–60 keV, and the second set focused on the range 5–20 keV. In both cases, we saw no evidence for photon-induced triggering of the 178m2Hf decay. Our measured cross sections placed upper limits for the process that are five-to-six orders of magnitude below the cross sections found by the Texas group.

1. C.B. Collins et. al., Phys. Rev. Lett. 82, 695 (1999); Europhys. Lett. 57, 667 (2002).
2. Science 283, 769 (1999); New Scientist, August 16, 2003, p4.
3. I. Ahmad et al., Phys. Rev. Lett. 87, 072503 (2001); Phys. Rev. C 67, 041305(R) (2003)

Picosecond Coherent Control of X-rays

M. F. DeCamp1, D. A. Reis1, P. H. Bucksbaum1, B. Adams2, J. M. Caraher1, R. Clarke1, C. W. S. Conover3, E. M. Dufresne1, R. Merlin1, V. Stoica1, J. K. Wahlstrand1

1 University of Michigan
2 Experimental Facilities Division, Argonne National Laboratory
3 Colby College

Synchrotrons produce continuous trains of closely spaced x-ray pulses. Application of such sources to the study of atomic-scale motion requires efficient modulation of these beams on time scales ranging from nanoseconds to femtoseconds. However, ultrafast x-ray modulators are not generally available. Here we report efficient subnanosecond coherent switching of synchrotron beams by using acoustic pulses in a crystal to modulate the anomalous low-loss transmission of x-ray pulses. The acoustic excitation transfers energy between two x-ray beams in a time shorter than the synchrotron pulse width of about 100 ps. Gigahertz modulation of the diffracted x-rays is also observed. We report different geometric arrangements, such as a switch based on the collision of two counter-propagating acoustic pulses. This doubles the x-ray modulation frequency and also provides a means of observing a localized transient strain inside an opaque material. We expect that these techniques could be scaled to produce subpicosecond pulses, through laser-generated coherent optical phonon modulation of X-ray diffraction in crystals. Such ultrafast capabilities have been demonstrated thus far only in laser-generated x-ray sources or through the use of x-ray streak cameras.

Coherent Bragg Rod Analysis (COBRA) of the Gd2O3/GaAs Interface Structure

Y. Yacoby1, M. Sowwan1, E. Stern2, J. O. Cross3, D. Brewe3, R. Pindak4, J. Pitney5, E. M. Dufresne6, and R. Clarke6

1 Hebrew University
2 University of Washington
3 Pacific Northwest Consortium Collaborative Access Team, Argonne National Laboratory,
4 Brookhaven National Laboratory
5 Center for Real-Time X-ray Studies, Argonne National Laboratory
6 University of Michigan

Obtaining accurate structural information on epitaxial films and interfaces is nowhere more critical than in semiconductor passivation layers, where details of the atomic structure and bonding determine the nature of the interface electronic states. Various non-destructive methods have been used to investigate the structure of films and interfaces, but their interpretation is model-dependent, leading occasionally to wrong conclusions. We have developed a new x-ray method for the direct determination of epitaxial structures: coherent Bragg rod analysis (COBRA). The usefulness of our technique is demonstrated by mapping, with atomic precision, the structure of the interfacial region of a Gd2O3 film grown epitaxially on a (100) GaAs substrate. Our findings reveal interesting behavior not previously suggested by existing structural methods, in particular a lock-in of the in-plane Gd atomic positions to those of the Ga/As atoms of the substrate. Moreover, we find that the bulk stacking of the Gd2O3 atomic layers is abandoned in favor of a new structure that is directly correlated with the stacking sequence of the substrate. These results have important implications for Gd2O3 as an effective passivation layer for GaAs. Our work shows that the COBRA technique, taking advantage of the brilliance of insertion device synchrotron x-ray sources, is widely applicable to epitaxial films and interfaces.

X-ray Photon Correlation Spectroscopy Studies of the Dynamics of Polymer Films

L. B. Lurio1, H. Kim2, A. Rühm3, J. K. Basu4, J. Lal5, S. G. J. Mochrie6, and S. K. Sinha7

1 Northern Illinois University
2 Sogang University
3 Max-Planck-Institut für Metallforschung
4 University of Illinois, Urbana-Champaign
5 Intense Pulsed Neutron Source, Argonne National Laboratory
6 Yale University
7 University of California, San Diego, and Los Alamos National Laboratory

X-ray photon correlation spectroscopy (XPCS) provides a method for the study of diffusive dynamics in polymers at molecular length scales. We have adapted XPCS to a reflection geometry in order to investigate dynamics in thin films of polystyrene. Detailed agreement is found between the observed wavevector dependence of the time-correlation functions and the predictions based on thermally driven capillary waves using the bulk values of viscosity and surface tension.

Coherent Diffraction Measurements of the Critical Scattering in Fe3Al

K. Laaziri1, M. Sutton1, G. B. Stephenson2, L. B. Lurio3

1 McGill University
2 Materials Science Division, Argonne National Laboratory
3 Northern Illinois University

By using a Fresnel zone plate to focus the beam, we were able to measure the time correlation functions associated with critical scattering for temperatures above the continuous phase transition in Fe3Al. These measurements provide a direct comparison to theories of dynamical scaling.

Structure of Liquid Iron at High Pressure

G. Shen1, V. B. Prakapenka1, M. L. Rivers1,2, S. R. Sutton1,2

1 Consortium for Advanced Radiation Sources, The University of Chicago
2 Department of Geophysical Sciences, The University of Chicago

Earth evolved into a layered body with a solid inner core and a liquid outer core, the latter accounting for about 96% of the core by volume. Dynamo action in the fluid outer core is responsible for sustaining the Earth’s magnetic field and the dynamics of this process are largely related to thermodynamic and transport properties of the outer core liquid. Information on the local structure of the liquid provides a basis for understanding numerous macroscopic properties. Until recently, information on structures of liquid iron under pressure has been largely restricted to theoretical studies. Direct experimental study of the structure of liquid iron has long been challenging because of experimental difficulties arising from the extreme conditions required to melt iron at relevant pressure. We present the results of structural studies on liquid iron up to 58 gigapascals measured by x-ray scattering in a laser-heated diamond anvil cell. In contrast to crystalline iron that undergoes phase transitions under pressure, the determined structure factor for liquid iron over the large pressure range preserves essentially the same shape along the melting curve. The results place important constraints on the thermodynamic and transport properties of liquid iron and the melting curve of iron.

Technically, the developed method should have broad applications for studying molten materials at extreme conditions. The highest pressure in this study is a record high pressure in structural investigations on molten materials, which becomes possible after integrated effort with the third-generation synchrotron and an optimized laser-heated diamond anvil cell system.

Time-Resolved Laue Studies on the E46Q Mutant of Photoactive Yellow Protein

S. Anderson, V. Srajer, R. Pahl, and K. Moffat

Consortium for Advanced Radiation Sources, The University of Chicago

Photoactive yellow protein (PYP) is a putative photoreceptor initially isolated from Halorhodospira halophila. We have used time-resolved crystallography to observe the development of structural change throughout the photocycle of the isosteric E46Q mutant of PYP. Fifty-four individual data sets were collected at 30 different time delays; the high redundancy and completeness in time allowed us to unambiguously visualize a novel early chromophore conformation along with very subtle tertiary structural changes. Although structural change occurs very rapidly on and around the chromophore, it takes milliseconds to fully progress throughout the photoreceptor.

Time-Resolved Ferroelectric Studies

C. Thompson1, M. E. M. Aanerud1, C. R. Gunderson1, G. B. Stephenson2, S. K. Streiffer2, G.–R. Bai2
1 Northern Illinois University
2 Materials Science Division, Argonne National Laboratory

In ferroelectric materials, domain configurations and structural response control their macroscopic physical properties, including electrical, optical, and mechanical. The cross-coupling relationships between these different properties are the basis of the use of ferroelectrics in the conversion between mechanical energy and electrical energy, as utilized in a wide variety of sensors, actuators, and transducers. Atomic displacements are also the physical origin of the ferroelectric polarization and are directly related to the behavior of ferroelectric elements in, for instance, non-volatile memories and to the attractive dielectric properties of ferroelectric films.

Time-resolved x-ray diffraction methods are being developed to study the structural response of ferroelectric and piezoelectric devices simultaneously with electrical stimulation. These methods allow observation of piezoresponse and polarization reversal dynamics in epitaxial ferroelectric thin films. Various strategies have been used for low-speed (millisecond) to high-speed (100 picosecond) time resolutions. Structural dynamics have been measured using time-resolved x-ray diffraction to track structural signatures of the polarization reorientation in ferroelectric and relaxor epitaxial thin films such as Pb(Zrx,Ti1-x)O3 (PZT) and Pb(Mg1/3Nb2/3)O3-PbTiO33 (PMN-PT) films on SrTiO3. We present experimental results that use a stroboscopic method exploiting the timing structure of the synchrotron ring to study lattice response transients in response to electrical stimulation. X-rays will provide an extremely powerful tool to study these systems, and future studies will benefit from the proposed nanoprobe beamline at the Advanced Photon Source at Argonne National Laboratory.

This work is supported by the U.S. Department of Energy under contract W-31-109-ENG-38, and the State of Illinois under HECA.

TiO2–Oligonucleotide Nanocomposites for Sequence-Specific Cleavage of Nucleic Acids and Intracellular Manipulation

T. Paunesku1,2, N. Stoji´cevi´c1,2,3, T. Rajh3, S. Vogt4, D. Legnini4, J. Maser4, B. Lai4, M. Thurnauer3, and G. Woloschak1,2

1 Northwestern University
2 Biosciences Division,
3 Chemistry Division
4 Experimental Facilities Division, Argonne National Laboratory

We have constructed and studied nanocomposites made of DNA oligonucleotides stably attached to TiO2 nanoparticles via dopamine. Excited TiO2 (upon accepting energy greater than 3.2 eV) generates electropositive holes that migrate onto the attached DNA. Accumulation of electropositive holes results in cleavage of the annealed nucleic acid.

The possibility of using TiO2-oligonucleotide nanocomposites for sequence-specific nucleic acid cleavage inside cells may advance genetic engineering/gene therapy and other intracellular manipulations into a new era. In order to accomplish this we need to study conditions of entry and retention of TiO2-oligonucleotide nanocomposites inside cells. Detection of K alpha x-ray fluorescence at 2-ID-E beamline of X-ray Operations and Research provides the most sensitive and speedy approach to intracellular Ti detection.

Following studies done in vitro and in cells we learned that the oligonucleotide nanocomposites hybridize with complementary DNA with high sequence specificity; that cleavage of DNA upon excitation of TiO2 by light or radiation does occur; and that these nanocomposites have the ability to enter and be retained in cells and subcellular organelles.

Phonon Softening in TiSe2

P. Zschack1, M. Holt1, H. Hong1, T.-C. Chiang1, and M.Y. Chou2

1University of Illinois at Urbana-Champaign
2Georgia Institute of Technology

Charge-density waves (CDW) in solids have been studied extensively for many years and provide a testing platform for concepts in electron-phonon interactions, electron correlations, and structural phase transitions. Among the most widely studied CDW systems are the layered transition metal dichalcogenides, such as TiSe2, which undergoes a CDW transition to form a 2x2x2 commensurate superlattice structure below the transition temperature of about 200K. At room temperature, neutron scattering has previously shown evidence of a Kohn anomaly in TiSe2 for the lowest phonon mode L1 at the Brillouin zone boundary. This mode was presumed to soften as the temperature is lowered. Using x-rays from the third-generation synchrotron radiation source at the Advanced Photon Source, we have performed detailed diffuse scattering measurements that demonstrate the frequency of the L1 phonon mode decreases gradually from its value at room temperature to zero at the transition temperature. This observation confirms the soft-mode concept that is central to understanding CDW phenomena in this type of material.

A Large-Scale Deposition of Novel Bacterial Structures to the Protein Data Bank

Structural GenomiX

The bacterial structure program at Structural GenomiX (SGX) resulted in the determination of 80 new bacterial structures, divided between 61 different sequences. SGX has decided to provide public domain access to this data by depositing all of these structures in the Protein Data Bank (PDB, Since the selection criteria for this program required that the targets would not have significant sequence homology to any previously solved structures, we anticipate that this data will provide researchers with a significant body of new structure-function information.

Previous publications from SGX resulted in the deposition of 8 structures to the PDB using the normal PDB deposition interface (ADIT), leaving 72 structures to deposit. This operation requires efficient methods to manage what could be a time-consuming task. The solution to this problem has been to generate, largely by automated procedures, mmCIF deposition files based on tags found in the standard mmCIF dictionary and in the newly developed mmCIF exchange dictionary. Mechanisms for creating these files were relatively easily implemented because SGX’s internal Structure Repository was already using mmCIF tags to capture structure validation statistics and data processing information (J. Badger, CCP4 newsletter, 39 [2001]). Similarly, mmCIF files containing structure factor lists and experimental phase information had already been created for all of these structures and will be provided to the PDB as part of the structure deposition.

The refinement statistics presented in these files were automatically calculated using SGX’s deposition system from the input atomic model and diffraction data, ensuring accuracy, completeness, and consistency. Similarly, the data processing statistics were parsed directly from log files output by the data processing programs. These structures have also been passed through structure validation software that contains criteria (R-factors, numbers of residues in the core of the Ramachandran plot, etc.) and a systematic battery of tests which ensure that the structure has been adequately refined and checked for errors on a per residue basis (J. Badger and J. Hendle, Acta Crystallogr. D 58, 284-291 [2002]). This previous work showed that, contrary to the belief that structures determined by high-throughput methods might contain larger numbers of significant errors than structures determined by more conventional laboratory practice, the systematic error-detection procedures that can be implemented in more controlled structure determination environments should lead to structures that will usually contain fewer than average numbers of errors.

We acknowledge the help of John Westbrook and Kyle Burkhardt of the RCSB PDB for assistance in developing the mmCIF file format to be used for these structure depositions.

Crystal Structure of the SARS Coronavirus Main Protease

J. B. Bonanno1, D. Lorimer1, R. Fowler1, R. Romero1, K.R. Rajashankar1, J. Hendle1, S. Gupta2, C.-L. Wei2, E. T. Liu2, S. K. Burley1, T. Harris1, J. M. Sauder1

1Structural GenomiX
2Genome Institute of Singapore

Severe Acute Respiratory Syndrome (SARS) achieved global notoriety as the first new epidemic of the twenty-first century. Three months after this new coronavirus was identified and characterized, the disease was declared contained, but only after it had infected over 8400 people from 30 countries and killed more than 800. The future threat of SARS remains unknown, although events at the end of this year should provide insights as to whether the virus will reoccur and how prevalent it will be. As a first step toward developing an anti-viral therapeutic using structure-based drug discovery, we determined the crystal structure of the SARS-CoV main protease to 1.86-Å resolution.