The development of four-dimensional ultrafast electron microscopy (4D UEM) has enabled not only observations of the ultrafast
dynamics of photon–matter interactions at the atomic scale with ultrafast resolution in image, diffraction, and energy space,
but photon–electron interactions in the field of nanoplasmonics and nanophotonics also have been captured by the related technique
of photon-induced near-field electron microscopy (PINEM) in image and energy space. Here we report a further extension in
the ongoing development of PINEM using a focused, nanometer-scale, electron beam in diffraction space for measurements of
infrared-light-induced PINEM. The energy resolution in diffraction mode is unprecedented, reaching 0.63 eV under the 200-keV
electron beam illumination, and separated peaks of the PINEM electron-energy spectrum induced by infrared light of wavelength
1,038 nm (photon energy 1.2 eV) have been well resolved for the first time, to our knowledge. In a comparison with excitation
by green (519-nm) pulses, similar first-order PINEM peak amplitudes were obtained for optical fluence differing by a factor
of more than 60 at the interface of copper metal and vacuum. Under high fluence, the nonlinear regime of IR PINEM was observed,
and its spatial dependence was studied. In combination with PINEM temporal gating and low-fluence infrared excitation, the
PINEM diffraction method paves the way for studies of structural dynamics in reciprocal space and energy space with high temporal
resolution.
Co-reporter:Byung-Kuk Yoo;John Meurig Thomas;Zixue Su
PNAS 2016 Volume 113 (Issue 3 ) pp:503-508
Publication Date(Web):2016-01-19
DOI:10.1073/pnas.1522869113
Understanding the dynamical nature of the catalytic active site embedded in complex systems at the atomic level is critical
to developing efficient photocatalytic materials. Here, we report, using 4D ultrafast electron microscopy, the spatiotemporal
behaviors of titanium and oxygen in a titanosilicate catalytic material. The observed changes in Bragg diffraction intensity
with time at the specific lattice planes, and with a tilted geometry, provide the relaxation pathway: the Ti4+=O2− double bond transformation to a Ti3+−O1− single bond via the individual atomic displacements of the titanium and the apical oxygen. The dilation of the double bond
is up to 0.8 Å and occurs on the femtosecond time scale. These findings suggest the direct catalytic involvement of the Ti3+−O1− local structure, the significance of nonthermal processes at the reactive site, and the efficient photo-induced electron
transfer that plays a pivotal role in many photocatalytic reactions.
Co-reporter:Mohammed T. Hassan;Haihua Liu;John Spencer Baskin
PNAS 2015 Volume 112 (Issue 42 ) pp:12944-12949
Publication Date(Web):2015-10-20
DOI:10.1073/pnas.1517942112
Ultrafast electron microscopy (UEM) is a pivotal tool for imaging of nanoscale structural dynamics with subparticle resolution
on the time scale of atomic motion. Photon-induced near-field electron microscopy (PINEM), a key UEM technique, involves the
detection of electrons that have gained energy from a femtosecond optical pulse via photon–electron coupling on nanostructures.
PINEM has been applied in various fields of study, from materials science to biological imaging, exploiting the unique spatial,
energy, and temporal characteristics of the PINEM electrons gained by interaction with a “single” light pulse. The further
potential of photon-gated PINEM electrons in probing ultrafast dynamics of matter and the optical gating of electrons by invoking
a “second” optical pulse has previously been proposed and examined theoretically in our group. Here, we experimentally demonstrate
this photon-gating technique, and, through diffraction, visualize the phase transition dynamics in vanadium dioxide nanoparticles.
With optical gating of PINEM electrons, imaging temporal resolution was improved by a factor of 3 or better, being limited
only by the optical pulse widths. This work enables the combination of the high spatial resolution of electron microscopy
and the ultrafast temporal response of the optical pulses, which provides a promising approach to attain the resolution of
few femtoseconds and attoseconds in UEM.
Co-reporter:Ebrahim Najafi;Timothy D. Scarborough;Jau Tang;Ahmed Zewail
Science 2015 Volume 347(Issue 6218) pp:164-167
Publication Date(Web):09 Jan 2015
DOI:10.1126/science.aaa0217
Traveling a long way past the junction
Diodes are central components of modern electronic circuits. They essentially consist of two semiconductors sandwiched together, with one deficient in electrons (p), the other enriched (n). Najafi et al. used ultrafast electron microscopy to study the dynamics in a silicon diode on a time scale of trillionths of a second. They discovered that when light excites the diode's charge carriers, those carriers migrate much farther past the p-n junction than standard models would imply. The authors explain the results using a ballistic transport model.
Co-reporter:Giovanni M. Vanacore, Renske M. van der Veen, and Ahmed H. Zewail
ACS Nano 2015 Volume 9(Issue 2) pp:1721
Publication Date(Web):January 30, 2015
DOI:10.1021/nn506524c
The coupling between electronic and nuclear degrees of freedom in low-dimensional, nanoscale systems plays a fundamental role in shaping many of their properties. Here, we report the disentanglement of axial and radial expansions of carbon nanotubes, and the direct role of electronic and vibrational excitations in determining such expansions. With subpicosecond and subpicometer resolutions, structural dynamics were explored by monitoring changes of the electron diffraction following an ultrafast optical excitation, whereas the transient behavior of the charge distribution was probed by time-resolved, electron-energy-loss spectroscopy. Our experimental results, and supporting density functional theory calculations, indicate that a population of the excited carriers in the antibonding orbitals of the nanotube walls drives a transient axial deformation in ∼1 ps; this deformation relaxes on a much longer time scale, 17 ps, by nonradiative decay. The electron-driven expansion is distinct from the phonon-driven dynamics observed along the radial direction, using the characteristic Bragg reflections; it occurs in 5 ps. These findings reveal the nonequilibrium distortion of the unit cell at early times and the role of the electron(phonon)-induced stress in the lattice dynamics of one-dimensional nanostructures.Keywords: 4D electron microscopy; carbon nanotubes; femtosecond electron-energy-loss spectroscopy; structural dynamics; ultrafast electron diffraction;
Co-reporter:Jianbo Hu, Giovanni M. Vanacore, Zhe Yang, Xiangshui Miao, and Ahmed H. Zewail
ACS Nano 2015 Volume 9(Issue 7) pp:6728
Publication Date(Web):June 2, 2015
DOI:10.1021/acsnano.5b01965
Phase-change materials (PCMs) represent the leading candidates for universal data storage devices, which exploit the large difference in the physical properties of their transitional lattice structures. On a nanoscale, it is fundamental to determine their performance, which is ultimately controlled by the speed limit of transformation among the different structures involved. Here, we report observation with atomic-scale resolution of transient structures of nanofilms of crystalline germanium telluride, a prototypical PCM, using ultrafast electron crystallography. A nonthermal transformation from the initial rhombohedral phase to the cubic structure was found to occur in 12 ps. On a much longer time scale, hundreds of picoseconds, equilibrium heating of the nanofilm is reached, driving the system toward amorphization, provided that high excitation energy is invoked. These results elucidate the elementary steps defining the structural pathway in the transformation of crystalline-to-amorphous phase transitions and describe the essential atomic motions involved when driven by an ultrafast excitation. The establishment of the time scales of the different transient structures, as reported here, permits determination of the possible limit of performance, which is crucial for high-speed recording applications of PCMs.Keywords: germanium telluride; Ge−Sb−Te alloy; phase transitions; phase-change materials; structural dynamics; ultrafast electron diffraction;
Light–matter interactions at the nanoscale are fundamental to the rapidly developing fields of plasmonics and nanophotonics. These fields hold the promise of advancing both the speed of computers along with communications and may also provide methods to create a new generation of ultrasensitive molecular biosensors. While there are a variety of techniques that can provide static images of these devices with suboptical wavelength precision there are only a few that are capable of capturing the ultrafast dynamics of electromagnetic fields interacting with or produced by nanomaterials. In this Perspective, we aim to introduce the reader to the newly developed field of 4D ultrafast electron microscopy (4D UEM), which provides a unique window into ultrafast dynamics at the nanoscale. We will describe the basic technique and how internal structural, bulk electronic, and surface near-field dynamics can all be obtained with nanometer and femtosecond resolutions. In addition, we will discuss how a variety of different ultrafast electron microscopes have been used to map the evolution of photonics-related phenomena. Throughout, we discuss the direction of research that will help advance the understanding of light–matter interactions near the atomic scale in both space and time.
Co-reporter:Haihua Liu, Oh-Hoon Kwon, Jau Tang, and Ahmed H. Zewail
Nano Letters 2014 Volume 14(Issue 2) pp:946-954
Publication Date(Web):January 6, 2014
DOI:10.1021/nl404354g
In this Letter, we introduce conical-scanning dark-field imaging in four-dimensional (4D) ultrafast electron microscopy to visualize single-particle dynamics of a polycrystalline ensemble undergoing phase transitions. Specifically, the ultrafast metal–insulator phase transition of vanadium dioxide is induced using laser excitation and followed by taking electron-pulsed, time-resolved images and diffraction patterns. The single-particle selectivity is achieved by identifying the origin of all constituent Bragg spots on Debye–Scherrer rings from the ensemble. Orientation mapping and dynamic scattering simulation of the electron diffraction patterns in the monoclinic and tetragonal phase during the transition confirm the observed behavior of Bragg spots change with time. We found that the threshold temperature for phase recovery increases with increasing particle sizes and we quantified the observation through a theoretical model developed for single-particle phase transitions. The reported methodology of conical scanning, orientation mapping in 4D imaging promises to be powerful for heterogeneous ensemble, as it enables imaging and diffraction at a given time with a full archive of structural information for each particle, for example, size, morphology, and orientation while minimizing radiation damage to the specimen.
Unlike in bulk materials, energy transport in low-dimensional and nanoscale systems may be governed by a coherent “ballistic” behavior of lattice vibrations, the phonons. If dominant, such behavior would determine the mechanism for transport and relaxation in various energy-conversion applications. In order to study this coherent limit, both the spatial and temporal resolutions must be sufficient for the length-time scales involved. Here, we report observation of the lattice dynamics in nanoscale quantum dots of gallium arsenide using ultrafast electron diffraction. By varying the dot size from h = 11 to 46 nm, the length scale effect was examined, together with the temporal change. When the dot size is smaller than the inelastic phonon mean-free path, the energy remains localized in high-energy acoustic modes that travel coherently within the dot. As the dot size increases, an energy dissipation toward low-energy phonons takes place, and the transport becomes diffusive. Because ultrafast diffraction provides the atomic-scale resolution and a sufficiently high time resolution, other nanostructured materials can be studied similarly to elucidate the nature of dynamical energy localization.
Co-reporter:María E. Corrales, Vincent Loriot, Garikoitz Balerdi, Jesús González-Vázquez, Rebeca de Nalda, Luis Bañares and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 19) pp:8812-8818
Publication Date(Web):24 Dec 2013
DOI:10.1039/C3CP54677B
The correlation between chemical structure and dynamics has been explored in a series of molecules with increasing structural complexity in order to investigate its influence on bond cleavage reaction times in a photodissociation event. Femtosecond time-resolved velocity map imaging spectroscopy reveals specificity of the ultrafast carbon–iodine (C–I) bond breakage for a series of linear (unbranched) and branched alkyl iodides, due to the interplay between the pure reaction coordinate and the rest of the degrees of freedom associated with the molecular structure details. Full-dimension time-resolved dynamics calculations support the experimental evidence and provide insight into the structure–dynamics relationship to understand structural control on time-resolved reactivity.
Microfluidic devices have recently become useful in commercial chemical synthesis. But what about fluid dynamics at the nanometer scale? Lorenz and Zewail used an electron microscope with nanosecond time resolution to capture images of molten lead flowing through a nanotube. They flash-melted the metal with a laser pulse to begin their flow measurements at a precise time point. The experiments offered insights into viscous friction as well as heat-transfer dynamics in a channel one-thousandth as wide as a strand of hair.
Helices are the “hydrogen atoms” of biomolecular complexity; the DNA/RNA double hairpin and protein α-helix ubiquitously form
the building blocks of life’s constituents at the nanometer scale. Nevertheless, the formation processes of these structures,
especially the dynamical pathways and rates, remain challenging to predict and control. Here, we present a general analytical
method for constructing dynamical free-energy landscapes of helices. Such landscapes contain information about the thermodynamic
stabilities of the possible macromolecular conformations, as well as about the dynamic connectivity, thus enabling the visualization
and computation of folding pathways and timescales. We elucidate the methodology using the folding of polyalanine, and demonstrate
that its α-helix folding kinetics is dominated by misfolded intermediates. At the physiological temperature of T = 298 K and midfolding time t = 250 ns, the fraction of structures in the native-state (α-helical) basin equals 22%, which is in good agreement with time-resolved
experiments and massively distributed, ensemble-convergent molecular-dynamics simulations. We discuss the prominent role of
β-strand–like intermediates in flight toward the native fold, and in relation to the primary conformational change precipitating
aggregation in some neurodegenerative diseases.
Four-dimensional multiple-cathode ultrafast electron microscopy is developed to enable the capture of multiple images at ultrashort
time intervals for a single microscopic dynamic process. The dynamic process is initiated in the specimen by one femtosecond
light pulse and probed by multiple packets of electrons generated by one UV laser pulse impinging on multiple, spatially distinct,
cathode surfaces. Each packet is distinctly recorded, with timing and detector location controlled by the cathode configuration.
In the first demonstration, two packets of electrons on each image frame (of the CCD) probe different times, separated by
19 picoseconds, in the evolution of the diffraction of a gold film following femtosecond heating. Future elaborations of this
concept to extend its capabilities and expand the range of applications of 4D ultrafast electron microscopy are discussed.
The proof-of-principle demonstration reported here provides a path toward the imaging of irreversible ultrafast phenomena
of materials, and opens the door to studies involving the single-frame capture of ultrafast dynamics using single-pump/multiple-probe,
embedded stroboscopic imaging.
Four-dimensional scanning ultrafast electron microscopy is used to investigate doping- and carrier-concentration-dependent
ultrafast carrier dynamics of the in situ cleaved single-crystalline GaAs(110) substrates. We observed marked changes in the
measured time-resolved secondary electrons depending on the induced alterations in the electronic structure. The enhancement
of secondary electrons at positive times, when the electron pulse follows the optical pulse, is primarily due to an energy
gain involving the photoexcited charge carriers that are transiently populated in the conduction band and further promoted
by the electron pulse, consistent with a band structure that is dependent on chemical doping and carrier concentration. When
electrons undergo sufficient energy loss on their journey to the surface, dark contrast becomes dominant in the image. At
negative times, however, when the electron pulse precedes the optical pulse (electron impact), the dynamical behavior of carriers
manifests itself in a dark contrast which indicates the suppression of secondary electrons upon the arrival of the optical
pulse. In this case, the loss of energy of material’s electrons is by collisions with the excited carriers. These results
for carrier dynamics in GaAs(110) suggest strong carrier–carrier scatterings which are mirrored in the energy of material’s
secondary electrons during their migration to the surface. The approach presented here provides a fundamental understanding
of materials probed by four-dimensional scanning ultrafast electron microscopy, and offers possibilities for use of this imaging
technique in the study of ultrafast charge carrier dynamics in heterogeneously patterned micro- and nanostructured material
surfaces and interfaces.
In materials, the nature of the strain–stress relationship, which is fundamental to their properties, is determined by both
the linear and nonlinear elastic responses. Whereas the linear response can be measured by various techniques, the nonlinear
behavior is nontrivial to probe and to reveal its nature. Here, we report the methodology of time-resolved Kikuchi diffraction
for mapping the (non)linear elastic response of nanoscale graphite following an ultrafast, impulsive strain excitation. It
is found that the longitudinal wave propagating along the c-axis exhibits echoes with a frequency of 9.1 GHz, which indicates the reflections of strain between the two surfaces of the
material with a speed of ∼4 km/s. Because Kikuchi diffraction enables the probing of strain in the transverse direction, we
also observed a higher-frequency mode at 75.5 GHz, which has a relatively long lifetime, on the order of milliseconds. The
fluence dependence and the polarization properties of this nonlinear mode are entirely different from those of the linear,
longitudinal mode, and here we suggest a localized breather motion in the a-b plane as the origin of the nonlinear shear dynamics. The approach presented in this contribution has the potential for a
wide range of applications because most crystalline materials exhibit Kikuchi diffraction.
Co-reporter:Anthony W. P. Fitzpatrick ; Ulrich J. Lorenz ; Giovanni M. Vanacore
Journal of the American Chemical Society 2013 Volume 135(Issue 51) pp:19123-19126
Publication Date(Web):December 6, 2013
DOI:10.1021/ja4115055
Cryo-electron microscopy is a form of transmission electron microscopy that has been used to determine the 3D structure of biological specimens in the hydrated state and with high resolution. We report the development of 4D cryo-electron microscopy by integrating the fourth dimension, time, into this powerful technique. From time-resolved diffraction of amyloid fibrils in a thin layer of vitrified water at cryogenic temperatures, we were able to detect picometer movements of protein molecules on a nanosecond time scale. Potential future applications of 4D cryo-electron microscopy are numerous, and some are discussed here.
Co-reporter:Renske M. van der Veen, Antoine Tissot, Andreas Hauser and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2013 vol. 15(Issue 20) pp:7831-7838
Publication Date(Web):19 Apr 2013
DOI:10.1039/C3CP51011E
Four-dimensional (4D) electron microscopy (EM) uniquely combines the high spatial resolution to pinpoint individual nano-objects, with the high temporal resolution necessary to address the dynamics of their laser-induced transformation. Here, using 4D-EM, we demonstrate the in situ irreversible transformation of individual nanoparticles of the molecular framework Fe(pyrazine)Pt(CN)4. The newly formed material exhibits an unusually large negative thermal expansion (i.e. contraction), which is revealed by time-resolved imaging and diffraction. Negative thermal expansion is a unique property exhibited by only few materials. Here we show that the increased flexibility of the metal–cyanide framework after the removal of the bridging pyrazine ligands is responsible for the negative thermal expansion behavior of the new material. This in situ visualization of single nanostructures during reactions should be extendable to other classes of reactive systems.
Co-reporter:Sang Tae Park;Anthony W. P. Fitzpatrick
PNAS 2013 Volume 110 (Issue 27 ) pp:10976-10981
Publication Date(Web):2013-07-02
DOI:10.1073/pnas.1309690110
Amyloid is an important class of proteinaceous material because of its close association with protein misfolding disorders
such as Alzheimer’s disease and type II diabetes. Although the degree of stiffness of amyloid is critical to the understanding
of its pathological and biological functions, current estimates of the rigidity of these β-sheet–rich protein aggregates range
from soft (108 Pa) to hard (1010 Pa) depending on the method used. Here, we use time-resolved 4D EM to directly and noninvasively measure the oscillatory
dynamics of freestanding, self-supporting amyloid beams and their rigidity. The dynamics of a single structure, not an ensemble,
were visualized in space and time by imaging in the microscope an amyloid–dye cocrystal that, upon excitation, converts light
into mechanical work. From the oscillatory motion, together with tomographic reconstructions of three studied amyloid beams,
we determined the Young modulus of these highly ordered, hydrogen-bonded β-sheet structures. We find that amyloid materials
are very stiff (109 Pa). The potential biological relevance of the deposition of such a highly rigid biomaterial in vivo are discussed.
Enhanced image contrast has been seen at graphene-layered steps a few nanometers in height by means of photon-induced near-field
electron microscopy (PINEM) using synchronous femtosecond pulses of light and electrons. The observed steps are formed by
the edges of graphene strips lying on the surface of a graphene substrate, where the strips are hundreds of nanometers in
width and many micrometers in length. PINEM measurements reflect the interaction of imaging electrons and induced (near) electric
fields at the steps, and this leads to a much higher contrast than that achieved in bright-field transmission electron microscopy
imaging of the same strips. Theory and numerical simulations support the experimental PINEM findings and elucidate the nature
of the electric field at the steps formed by the graphene layers. These results extend the range of applications of the experimental
PINEM methodology, which has previously been demonstrated for spherical, cylindrical, and triangular nanostructures, to shapes
of high aspect ratio (rectangular strips), as well as into the regime of atomic layer thicknesses.
We present a technique for in situ visualization of the biomechanics of DNA structural networks using 4D electron microscopy.
Vibrational oscillations of the DNA structure are excited mechanically through a short burst of substrate vibrations triggered
by a laser pulse. Subsequently, the motion is probed with electron pulses to observe the impulse response of the specimen
in space and time. From the frequency and amplitude of the observed oscillations, we determine the normal modes and eigenfrequencies
of the structures involved. Moreover, by selective “nano-cutting” at a given point in the network, it was possible to obtain
Young’s modulus, and hence the stiffness, of the DNA filament at that position. This experimental approach enables nanoscale
mechanics studies of macromolecules and should find applications in other domains of biological networks such as origamis.
Co-reporter:David J. Flannigan and Ahmed H. Zewail
Accounts of Chemical Research 2012 Volume 45(Issue 10) pp:1828
Publication Date(Web):September 11, 2012
DOI:10.1021/ar3001684
The transmission electron microscope (TEM) is a powerful tool enabling the visualization of atoms with length scales smaller than the Bohr radius at a factor of only 20 larger than the relativistic electron wavelength of 2.5 pm at 200 keV. The ability to visualize matter at these scales in a TEM is largely due to the efforts made in correcting for the imperfections in the lens systems which introduce aberrations and ultimately limit the achievable spatial resolution. In addition to the progress made in increasing the spatial resolution, the TEM has become an all-in-one characterization tool. Indeed, most of the properties of a material can be directly mapped in the TEM, including the composition, structure, bonding, morphology, and defects. The scope of applications spans essentially all of the physical sciences and includes biology.Until recently, however, high resolution visualization of structural changes occurring on sub-millisecond time scales was not possible. In order to reach the ultrashort temporal domain within which fundamental atomic motions take place, while simultaneously retaining high spatial resolution, an entirely new approach from that of millisecond-limited TEM cameras had to be conceived. As shown below, the approach is also different from that of nanosecond-limited TEM, whose resolution cannot offer the ultrafast regimes of dynamics. For this reason “ultrafast electron microscopy” is reserved for the field which is concerned with femtosecond to picosecond resolution capability of structural dynamics.In conventional TEMs, electrons are produced by heating a source or by applying a strong extraction field. Both methods result in the stochastic emission of electrons, with no control over temporal spacing or relative arrival time at the specimen. The timing issue can be overcome by exploiting the photoelectric effect and using pulsed lasers to generate precisely timed electron packets of ultrashort duration. The spatial and temporal resolutions achievable with short intense pulses containing a large number of electrons, however, are limited to tens of nanometers and nanoseconds, respectively. This is because Coulomb repulsion is significant in such a pulse, and the electrons spread in space and time, thus limiting the beam coherence. It is therefore not possible to image the ultrafast elementary dynamics of complex transformations. The challenge was to retain the high spatial resolution of a conventional TEM while simultaneously enabling the temporal resolution required to visualize atomic-scale motions.In this Account, we discuss the development of four-dimensional ultrafast electron microscopy (4D UEM) and summarize techniques and applications that illustrate the power of the approach. In UEM, images are obtained either stroboscopically with coherent single-electron packets or with a single electron bunch. Coulomb repulsion is absent under the single-electron condition, thus permitting imaging, diffraction, and spectroscopy, all with high spatiotemporal resolution, the atomic scale (sub-nanometer and femtosecond). The time resolution is limited only by the laser pulse duration and energy carried by the electron packets; the CCD camera has no bearing on the temporal resolution. In the regime of single pulses of electrons, the temporal resolution of picoseconds can be attained when hundreds of electrons are in the bunch.The applications given here are selected to highlight phenomena of different length and time scales, from atomic motions during structural dynamics to phase transitions and nanomechanical oscillations. We conclude with a brief discussion of emerging methods, which include scanning ultrafast electron microscopy (S-UEM), scanning transmission ultrafast electron microscopy (ST-UEM) with convergent beams, and time-resolved imaging of biological structures at ambient conditions with environmental cells.
Co-reporter:Aycan Yurtsever, Sascha Schaefer, and Ahmed H. Zewail
Nano Letters 2012 Volume 12(Issue 7) pp:3772-3777
Publication Date(Web):June 5, 2012
DOI:10.1021/nl301644t
Complex structural dynamics at the nanoscale requires sufficiently small probes to be visualized. In conventional imaging using electron microscopy, the dimension of the probe is large enough to cause averaging over the structures present. However, by converging ultrafast electron bunches, it is possible to select a single nanoscale structure and study the dynamics, either in the image or using electron diffraction. Moreover, the span of incident wave vectors in a convergent beam enables sensitivity levels and information contents beyond those of parallel-beam illumination with a single wave vector Bragg diffraction. Here, we report the observation of propagating strain waves using ultrafast Kikuchi diffraction from nanoscale volumes within a wedge-shaped silicon single crystal. It is found that the heterogeneity of the strain in the lateral direction is only 100 nm. The transient elastic wave gives rise to a coherent oscillation with a period of 30 ps and with an envelope that has a width of 140 ps. The origin of this elastic deformation is theoretically examined using finite element analysis; it is identified as propagating shear waves. The wedge-shaped structure, unlike parallel-plate structure, is the key behind the traveling nature of the waves as its angle permits “transverse” propagation; the parallel-plate structure only exhibits the “longitudinal” motion. The studies reported suggest extension to a range of applications for nanostructures of different shapes and for exploring their ultrafast eigen-modes of stress–strain profiles.
Electric fields of nanoscale particles are fundamental to our understanding of nanoplasmonics and nanophotonics. Success has been made in developing methods to probe the effect of their presence, but it remains difficult to directly image optically induced electric fields at the nanoscale and especially when ensembles of particles are involved. Here, using ultrafast electron microscopy, we report the space-time visualization of photon-induced electric fields for ensembles of silver nanoparticles having different sizes, shapes, and separations. The high-field-of-view measurements enable parallel processing of many particles in the ensemble with high throughput of information. Directly in the image, the evanescent fields are observed and visualized when the particles are polarized with the optical excitation. Because the particle size is smaller than the wavelength of light, the near-fields are those of nanoplasmonics and are precursors of far-field nanophotonics. The reported results pave the way for quantitative studies of fields in ensembles of complex morphologies with the nanoparticles being embedded or interfacial.
Co-reporter:Aycan Yurtsever, J. Spencer Baskin, and Ahmed H. Zewail
Nano Letters 2012 Volume 12(Issue 9) pp:5027-5032
Publication Date(Web):August 8, 2012
DOI:10.1021/nl302824f
Particle interactions are fundamental to our understanding of nanomaterials and biological assemblies. Here, we report on the visualization of entangled particles, separated by as large as 70 nm, and the discovery of channels in their near-fields. For silver nanoparticles, the induced field of each particle extends to 50–100 nm, but when particles are brought close in separation we observe channels as narrow as 6 nm, a width that is 2 orders of magnitude smaller than the incident field wavelength. The channels’ directions can be controlled by the polarization of the incident field, particle size, and separation. For this direct visualization of these nanoscopic near-fields, the high spatial, temporal, and energy resolutions needed were hitherto not possible without the methodology given here. This methodology, we anticipate, paves the way for further fundamental studies of particle entanglement and for possible applications spanning materials and macromolecular assemblies.
Journal of the American Chemical Society 2012 Volume 134(Issue 22) pp:9146-9149
Publication Date(Web):May 16, 2012
DOI:10.1021/ja304042r
We report the anisotropic atomic expansion dynamics of multi-walled carbon nanotubes, using 4D electron microscopy. From time-resolved diffraction on the picosecond to millisecond scale, following ultrafast heating at the rate of 1013 K/s, it is shown that nanotubes expand only in the radial (intertubule) direction, whereas no significant change is observed in the intratubular axial or equatorial dimensions. The non-equilibrium heating occurs on an ultrafast time scale, indicating that the anisotropy is the result of an efficient electron–lattice coupling and is maintained up to equilibration. The recovery time, which measures the heat dissipation rate for equilibration, was found to be on the order of ∼100 μs. This recovery is reproduced theoretically by considering the composite specimen–substrate heat exchange.
In this Letter, we discuss the use of photon-induced near field electron microscopy (PINEM) to reach new limits of temporal and spatial resolutions. We invoke two optical femtosecond pulses, one of them is for the usual clocking of dynamical change but the second one is for gating (slicing) the imaging-electron continuous or pulsed beam. It is shown that in both cases the resolution becomes that of the optical gating pulse and not of the electron one. We also show that by using the near field of a nanoparticle it is possible to enhance contrast in imaging of materials and including biological structures.
To find the native conformation (fold), proteins sample a subspace that is typically hundreds of orders of magnitude smaller
than their full conformational space. Whether such fast folding is intrinsic or the result of natural selection, and what
is the longest foldable protein, are open questions. Here, we derive the average conformational degeneracy of a lattice polypeptide
chain in water and quantitatively show that the constraints associated with hydrophobic forces are themselves sufficient to
reduce the effective conformational space to a size compatible with the folding of proteins up to approximately 200 amino
acids long within a biologically reasonable amount of time. This size range is in general agreement with the experimental
protein domain length distribution obtained from approximately 1,200 proteins. Molecular dynamics simulations of the Trp-cage
protein confirm this picture on the free energy landscape. Our analytical and computational results are consistent with a
model in which the length and time scales of protein folding, as well as the modular nature of large proteins, are dictated
primarily by inherent physical forces, whereas natural selection determines the native state.
The Journal of Physical Chemistry A 2012 Volume 116(Issue 46) pp:11128-11133
Publication Date(Web):June 28, 2012
DOI:10.1021/jp304534n
Electrons and photons, when interacting via a nanostructure, produce a new way of imaging in space and time, termed photon-induced near field electron microscopy or PINEM [Barwick et al. Nature2009, 462, 902]. The phenomenon was described by considering the evanescent field produced by the nanostructure, but quantification of the experimental results was achieved by solving the Schrödinger equation for the interaction of the three bodies. The question remained, is the nonrelativistic formulation sufficient for this description? Here, relativistic and nonrelativistic quantum mechanical formulations are compared for electron–photon interaction mediated by nanostructures, and it is shown that there is an exact equivalence for the two formulations. The nonrelativistic formulation was found to be valid in the relativistic regime when using in the former formulation the relativistically corrected velocity (and the corresponding values of momentum and energy). In the PINEM experiment, 200 keV electrons were utilized, giving the experimental (relativistically corrected) velocity to be 0.7c(v without relativistic correction is 0.885c). When this value (0.7c), together with those of the corresponding momentum (pc = mv) and energy (Ec = (1/2)mv2), is used in the first order solution of the Schrödinger formulation, an exact equivalence is obtained.
Co-reporter:J. Spencer Baskin, Hyun Soon Park, and Ahmed H. Zewail
Nano Letters 2011 Volume 11(Issue 5) pp:2183-2191
Publication Date(Web):April 22, 2011
DOI:10.1021/nl200930a
Nanomusical systems, nanoharp and nanopiano, fabricated as arrays of cantilevers by focused ion beam milling of a layered Ni/Ti/Si3N4 thin film, have been investigated in 4D electron microscopy. With the imaging and selective femtosecond and nanosecond control combinations, full characterization of the amplitude and phase of the resonant response of a particular cantilever relative to the optical pulse train was possible. Using a high repetition rate, low energy optical pulse train for selective, resonant excitation, coupled with pulsed and steady-state electron imaging for visualization in space and time, both the amplitude on the nanoscale and resonance of motion on the megahertz scale were resolved for these systems. Tilting of the specimen allowed in-plane and out-of-plane cantilever bending and cantilever torsional motions to be identified in stroboscopic measurements of impulsively induced free vibration. Finally, the transient, as opposed to steady state, thermostat effect was observed for the layered nanocantilevers, with a sufficiently sensitive response to demonstrate suitability for in situ use in thin-film temperature measurements requiring resolutions of <10 K and 10 μm on time scales here mechanically limited to microseconds and potentially at shorter times.
Journal of the American Chemical Society 2011 Volume 133(Issue 6) pp:1730-1733
Publication Date(Web):January 21, 2011
DOI:10.1021/ja110952k
We report direct visualization of irreversible chemical reactions in space and time with 4D electron microscopy. Specifically, transient structures are imaged following electron transfer in copper-tetracyanoquinodimethane [Cu(TCNQ)] crystals, and the oxidation/reduction process, which is irreversible, is elucidated using the single-shot operation mode of the microscope. We observed the fast, initial structural rearrangement due to Cu+ reduction and the slower growth of metallic Cu0 nanocrystals (Ostwald ripening) following initiation of the reaction with a pulse of visible light. The mechanism involves electron transfer from TCNQ anion-radical to Cu+, morphological changes, and thermally driven growth of discrete Cu0 nanocrystals embedded in an amorphous carbon skeleton of TCNQ. This in situ visualization of structures during reactions should be extendable to other classes of reactive systems.
Co-reporter:Omar F. Mohammed ; Ding-Shyue Yang ; Samir Kumar Pal
Journal of the American Chemical Society 2011 Volume 133(Issue 20) pp:7708-7711
Publication Date(Web):May 3, 2011
DOI:10.1021/ja2031322
The continuous electron beam of conventional scanning electron microscopes (SEM) limits the temporal resolution required for the study of ultrafast dynamics of materials surfaces. Here, we report the development of scanning ultrafast electron microscopy (S-UEM) as a time-resolved method with resolutions in both space and time. The approach is demonstrated in the investigation of the dynamics of semiconducting and metallic materials visualized using secondary-electron images and backscattering electron diffraction patterns. For probing, the electron packet was photogenerated from the sharp field-emitter tip of the microscope with a very low number of electrons in order to suppress space–charge repulsion between electrons and reach the ultrashort temporal resolution, an improvement of orders of magnitude when compared to the traditional beam-blanking method. Moreover, the spatial resolution of SEM is maintained, thus enabling spatiotemporal visualization of surface dynamics following the initiation of change by femtosecond heating or excitation. We discuss capabilities and potential applications of S-UEM in materials and biological science.
Journal of the American Chemical Society 2011 Volume 133(Issue 42) pp:17072-17086
Publication Date(Web):October 5, 2011
DOI:10.1021/ja207722k
Among the macromolecular patterns of biological significance, right-handed α-helices are perhaps the most abundant structural motifs. Here, guided by experimental findings, we discuss both ultrafast initial steps and longer-time-scale structural dynamics of helix–coil transitions induced by a range of temperature jumps in large, isolated macromolecular ensembles of an α-helical protein segment thymosin β9 (Tβ9), and elucidate the comprehensive picture of (un)folding. In continuation of an earlier theoretical work from this laboratory that utilized a simplistic structure-scrambling algorithm combined with a variety of self-avoidance thresholds to approximately model helix–coil transitions in Tβ9, in the present contribution we focus on the actual dynamics of unfolding as obtained from massively distributed ensemble-convergent MD simulations which provide an unprecedented scope of information on the nature of transient macromolecular structures, and with atomic-scale spatiotemporal resolution. In addition to the use of radial distribution functions of ultrafast electron diffraction (UED) simulations in gaining an insight into the elementary steps of conformational interconversions, we also investigate the structural dynamics of the protein via the native (α-helical) hydrogen bonding contact metric which is an intuitive coarse graining approach. Importantly, the decay of α-helical motifs and the (globular) conformational annealing in Tβ9 occur consecutively or competitively, depending on the magnitude of temperature jump.
Journal of the American Chemical Society 2011 Volume 133(Issue 28) pp:10732-10735
Publication Date(Web):May 26, 2011
DOI:10.1021/ja203821y
We report the development of 4D scanning transmission ultrafast electron microscopy (ST-UEM). The method was demonstrated in the imaging of silver nanowires and gold nanoparticles. For the wire, the mechanical motion and shape morphological dynamics were imaged, and from the images we obtained the resonance frequency and the dephasing time of the motion. Moreover, we demonstrate here the simultaneous acquisition of dark-field images and electron energy loss spectra from a single gold nanoparticle, which is not possible with conventional methods. The local probing capabilities of ST-UEM open new avenues for probing dynamic processes, from single isolated to embedded nanostructures, without being affected by the heterogeneous processes of ensemble-averaged dynamics. Such methodology promises to have wide-ranging applications in materials science and in single-particle biological imaging.
Co-reporter:Dongping Zhong, Samir Kumar Pal, Ahmed H. Zewail
Chemical Physics Letters 2011 Volume 503(1–3) pp:1-11
Publication Date(Web):8 February 2011
DOI:10.1016/j.cplett.2010.12.077
Abstract
In this overview, we provide a critique of the hydration dynamics of macromolecules, particularly those of protein and DNA. Only in the past decade has femtosecond spectroscopy enabled direct access to the ultrafast dynamical motion of surface water. With the wealth of results from this spectroscopic technique, NMR, and neutron scattering, it is now established that hydration is indeed an ultrafast phenomenon, and in this sense the ‘iceberg model’ is invalid. Here, we overview the experimental and the theoretical studies, hoping to clarify the confusion resulting from some recent MD simulations. We maintain that there are two types of water hydration, those that reorient in the vicinity of the surface and those which are ordered, however in dynamic interaction with the protein.
Co-reporter:Sascha Schäfer, Wenxi Liang, Ahmed H. Zewail
Chemical Physics Letters 2011 Volume 515(4–6) pp:278-282
Publication Date(Web):27 October 2011
DOI:10.1016/j.cplett.2011.09.042
Abstract
By employing ultrafast electron crystallography in a transmission geometry for ultra-thin (2–3 nm) gold, here we show that structural dynamics of the transverse atomic motions and the atomic displacements around the equilibrium position can be separated from the measured change in Bragg diffraction, the positions and intensities of the peaks, respectively. The rate of intensity change provides the electron-lattice equilibration time whereas the observed lattice expansion, which occurs on a slower time scale, maps the delayed response of transverse lattice strain. These textbook-type results provide the microscopic stress–strain profile that is critical for understanding dynamical deformations and the effect of morphological structures at surfaces.
Macromolecular conformation dynamics, which span a wide range of time scales, are fundamental to the understanding of properties
and functions of their structures. Here, we report direct imaging of structural dynamics of helical macromolecules over the
time scales of conformational dynamics (ns to subsecond) by means of four-dimensional (4D) electron microscopy in the single-pulse
and stroboscopic modes. With temporally controlled electron dosage, both diffraction and real-space images are obtained without
irreversible radiation damage. In this way, the order-disorder transition is revealed for the organic chain polymer. Through
a series of equilibrium-temperature and temperature-jump dependencies, it is shown that the metastable structures and entropy
of conformations can be mapped in the nonequilibrium region of a “funnel-like” free-energy landscape. The T-jump is introduced through a substrate (a “hot plate” type arrangement) because only the substrate is made to absorb the
pulsed energy. These results illustrate the promise of ultrafast 4D imaging for other applications in the study of polymer
physics as well as in the visualization of biological phenomena.
Coherent atomic motions in materials can be revealed using time-resolved X-ray and electron Bragg diffraction. Because of
the size of the beam used, typically on the micron scale, the detection of nanoscale propagating waves in extended structures hitherto has not been reported. For elastic waves of complex motions, Bragg intensities
contain all polarizations and they are not straightforward to disentangle. Here, we introduce Kikuchi diffraction dynamics,
using convergent-beam geometry in an ultrafast electron microscope, to selectively probe propagating transverse elastic waves
with nanoscale resolution. It is shown that Kikuchi band shifts, which are sensitive only to the tilting of atomic planes,
reveal the resonance oscillations, unit cell angular amplitudes, and the polarization directions. For silicon, the observed
wave packet temporal envelope (resonance frequency of 33 GHz), the out-of-phase temporal behavior of Kikuchi’s edges, and
the magnitude of angular amplitude (0.3 mrad) and polarization elucidate the nature of the motion: one that preserves the mass density (i.e., no compression or expansion) but leads to
sliding of planes in the antisymmetric shear eigenmode of the elastic waveguide. As such, the method of Kikuchi diffraction
dynamics, which is unique to electron imaging, can be used to characterize the atomic motions of propagating waves and their
interactions with interfaces, defects, and grain boundaries at the nanoscale.
Co-reporter:Milo M. Lin;Omar F. Mohammed;Gouri S. Jas
PNAS 2011 Volume 108 (Issue 40 ) pp:
Publication Date(Web):2011-10-04
DOI:10.1073/pnas.1113649108
As the simplest and most prevalent motif of protein folding, α-helix initiation is the starting point of macromolecular complexity.
In this work, helix initiation was directly measured via ultrafast temperature-jump spectroscopy on the smallest possible
helix nucleus for which only the first turn is formed. The rate’s dependence on sequence, length, and temperature reveals
the fastest possible events in protein folding dynamics, and it was possible to separate the rate-limiting torsional (conformational)
diffusion from the fast annealing of the helix. An analytic coarse-grained model for this process, which predicts the initiation
rate as a function of temperature, confirms this picture. Moreover, the stipulations of the model were verified by ensemble-converging
all-atom molecular dynamics simulations, which reproduced both the picosecond annealing and the nanosecond diffusion processes
observed experimentally.
Co-reporter:Hyun Soon Park, J. Spencer Baskin and Ahmed H. Zewail
Nano Letters 2010 Volume 10(Issue 9) pp:3796-3803
Publication Date(Web):August 25, 2010
DOI:10.1021/nl102861e
Magnetization reversal is an important topic of research in the fields of both basic and applied ferromagnetism. For the study of magnetization reversal dynamics and magnetic domain wall (DW) motion in ferromagnetic thin films, imaging techniques are indispensable. Here, we report 4D imaging of DWs by the out-of-focus Fresnel method in Lorentz ultrafast electron microscopy (UEM), with in situ spatial and temporal resolutions. The temporal change in magnetization, as revealed by changes in image contrast, is clocked using an impulsive optical field to produce structural deformation of the specimen, thus modulating magnetic field components in the specimen plane. Directly visualized are DW nucleation and subsequent annihilation and oscillatory reappearance (periods of 32 and 45 ns) in nickel films on two different substrates. For the case of Ni films on a Ti/Si3N4 substrate, under conditions of minimum residual external magnetic field, the oscillation is associated with a unique traveling wave train of periodic magnetization reversal. The velocity of DW propagation in this wave train is measured to be 172 m/s with a wavelength of 7.8 μm. The success of this study demonstrates the promise of Lorentz UEM for real-space imaging of spin switching, ferromagnetic resonance, and laser-induced demagnetization in ferromagnetic nanostructures.
Co-reporter:David J. Flannigan and Ahmed H. Zewail
Nano Letters 2010 Volume 10(Issue 5) pp:1892-1899
Publication Date(Web):April 8, 2010
DOI:10.1021/nl100733h
With ultrafast electron microscopy (UEM), we report observation of the nanoscopic crystallization of amorphous silicon nitride, and the ultrashort optomechanical motion of the crystalline silicon nitride at the interface of an adhering carbon nanotube network. The in situ static crystallization of the silicon nitride occurs only in the presence of an adhering nanotube network, thus indicating their mediating role in reaching temperatures close to 1000 °C when exposed to a train of laser pulses. Under such condition, 4D visualization of the optomechanical motion of the specimen was followed by quantifying the change in diffraction contrast of crystalline silicon nitride, to which the nanotube network is bonded. The direction of the motion was established from a tilt series correlating the change in displacement with both the tilt angle and the response time. Correlation of nanoscopic motion with the picosecond atomic-scale dynamics suggests that electronic processes initiated in the nanotubes are responsible for the initial ultrafast optomechanical motion. The time scales accessible to UEM are 12 orders of magnitude shorter than those traditionally used to study the optomechanical motion of carbon nanotube networks, thus allowing for distinctions between the different electronic and thermal mechanisms to be made.
Co-reporter:Oh-Hoon Kwon, Hyun Soon Park, J. Spencer Baskin and Ahmed H. Zewail
Nano Letters 2010 Volume 10(Issue 8) pp:3190-3198
Publication Date(Web):July 22, 2010
DOI:10.1021/nl102141t
Direct electron imaging with sufficient time resolution is a powerful tool for visualizing the three-dimensional (3D) mechanical motion and resolving the four-dimensional (4D) trajectories of many different components of a nanomachine, e.g., a NEMS device. Here, we report a nanoscale nonchaotic motion of a nano- and microstructured NiTi shape memory alloy in 4D electron microscopy. A huge amplitude oscillatory mechanical motion following laser heating is observed repetitively, likened to a 3D motion of a conductor’s baton. By time-resolved 4D stereographic reconstruction of the motion, prominent vibrational frequencies (3.0, 3.8, 6.8, and 14.5 MHz) are fully characterized, showing evidence of nonlinear behavior. Moreover, it is found that a stress (fluence)−strain (displacement) profile shows nonlinear elasticity. The observed resonances of the nanostructure are reminiscent of classical molecular quasi-periodic behavior, but here both the amplitude and frequency of the motion are visualized using ultrafast electron microscopy.
In this letter, we report a novel method of visualizing nanoscale friction in space and time using ultrafast electron microscopy (UEM). The methodology is demonstrated for a nanoscale movement of a single crystal beam on a thin amorphous membrane of silicon nitride. The movement results from the elongation of the crystal beam, which is initiated by a laser (clocking) pulse, and we examined two types of beams: those that are free of friction and the others which are fixed on the substrate. From observations of image change with time we are able to decipher the nature of microscopic friction at the solid−solid interface: smooth-sliding and periodic slip-stick friction. At the molecular and nanoscale level, and when a force parallel to the surface (expansion of the beam) is applied, the force of gravity as a (perpendicular) load cannot explain the observed friction. An additional effective load being 6 orders of magnitude larger than that due to gravity is attributed to Coulombic/van der Waals adhesion at the interface. For the case under study, metal−organic crystals, the gravitational force is on the order of piconewtons whereas the static friction force is 0.5 μN and dynamic friction is 0.4 μN; typical beam expansions are 50 nm/nJ for the free beam and 10 nm/nJ for the fixed beam. The method reported here should have applications for other materials, and for elucidating the origin of periodic and chaotic friction and their relevance to the efficacy of nano(micro)-scale devices.
Co-reporter:Sascha Schäfer, Wenxi Liang, Ahmed H. Zewail
Chemical Physics Letters 2010 Volume 493(1–3) pp:11-18
Publication Date(Web):17 June 2010
DOI:10.1016/j.cplett.2010.04.049
Ultrafast electron microscopy and diffraction provide direct visualization of structural dynamics with atomic scale resolution. In surface diffraction studies, it may have been assumed that the generation of transient electric fields could mask some features of structural dynamics. Here, we show that such an effect is irrelevant when ultrafast electron microscopy is invoked. It is also demonstrated that for the diffraction investigation of surfaces at grazing angles it is straightforward to observe the structural dynamics provided that simple controls are made for diffraction dependencies on order and intensity, and a comparison with the behavior of the undiffracted beam.Structural dynamics with atomic-scale resolution are considered for both microscopy and surface crystallography. Experimental and theoretical results elucidate the insignificant role of transient electric fields in microscopy and show how structural dynamics can unambiguously be determined in diffraction from surfaces.
Progress has been made in the development of four-dimensional ultrafast electron microscopy, which enables space-time imaging
of structural dynamics in the condensed phase. In ultrafast electron microscopy, the electrons are accelerated, typically
to 200 keV, and the microscope operates in the transmission mode. Here, we report the development of scanning ultrafast electron
microscopy using a field-emission-source configuration. Scanning of pulses is made in the single-electron mode, for which
the pulse contains at most one or a few electrons, thus achieving imaging without the space-charge effect between electrons,
and still in ten(s) of seconds. For imaging, the secondary electrons from surface structures are detected, as demonstrated
here for material surfaces and biological specimens. By recording backscattered electrons, diffraction patterns from single
crystals were also obtained. Scanning pulsed-electron microscopy with the acquired spatiotemporal resolutions, and its efficient
heat-dissipation feature, is now poised to provide in situ 4D imaging and with environmental capability.
Co-reporter:Oh-Hoon Kwon;Tae Hyeon Yoo;Christina M. Othon;James A. Van Deventer;David A. Tirrell
PNAS 2010 Volume 107 (Issue 40 ) pp:17101-17106
Publication Date(Web):2010-10-05
DOI:10.1073/pnas.1011569107
Water-protein interactions dictate many processes crucial to protein function including folding, dynamics, interactions with
other biomolecules, and enzymatic catalysis. Here we examine the effect of surface fluorination on water-protein interactions.
Modification of designed coiled-coil proteins by incorporation of 5,5,5-trifluoroleucine or (4S)-2-amino-4-methylhexanoic acid enables systematic examination of the effects of side-chain volume and fluorination on solvation
dynamics. Using ultrafast fluorescence spectroscopy, we find that fluorinated side chains exert electrostatic drag on neighboring
water molecules, slowing water motion at the protein surface.
Proceedings of the National Academy of Sciences 2010 107(22) pp:9933-9937
Publication Date(Web):May 17, 2010
DOI:10.1073/pnas.1005653107
Advances in the imaging of biological structures with transmission electron microscopy continue to reveal information at the
nanometer length scale and below. The images obtained are static, i.e., time-averaged over seconds, and the weak contrast
is usually enhanced through sophisticated specimen preparation techniques and/or improvements in electron optics and methodologies.
Here we report the application of the technique of photon-induced near-field electron microscopy (PINEM) to imaging of biological
specimens with femtosecond (fs) temporal resolution. In PINEM, the biological structure is exposed to single-electron packets
and simultaneously irradiated with fs laser pulses that are coincident with the electron pulses in space and time. By electron
energy-filtering those electrons that gained photon energies, the contrast is enhanced only at the surface of the structures
involved. This method is demonstrated here in imaging of protein vesicles and whole cells of Escherichia coli, both are not absorbing the photon energy, and both are of low-Z contrast. It is also shown that the spatial location of contrast enhancement can be controlled via laser polarization, time
resolution, and tomographic tilting. The high-magnification PINEM imaging provides the nanometer scale and the fs temporal
resolution. The potential of applications is discussed and includes the study of antibodies and immunolabeling within the
cell.
Co-reporter:David J. Flannigan, Peter C. Samartzis, Aycan Yurtsever and Ahmed H. Zewail
Nano Letters 2009 Volume 9(Issue 2) pp:875-881
Publication Date(Web):January 9, 2009
DOI:10.1021/nl803770e
The function of many nano- and microscale systems is revealed when they are visualized in both space and time. Here, we report our first observation, using four-dimensional (4D) electron microscopy, of the nanomechanical motions of cantilevers. From the observed oscillations of nanometer displacements as a function of time, for free-standing beams, we are able to measure the frequency of modes of motion and determine Young’s elastic modulus and the force and energy stored during the optomechanical expansions. The motion of the cantilever is triggered by molecular charge redistribution as the material, single-crystal organic semiconductor, switches from the equilibrium to the expanded structure. For these material structures, the expansion is colossal, typically reaching the micrometer scale, the modulus is 2 GPa, the force is 600 μN, and the energy is 200 pJ. These values translate to a large optomechanical efficiency (minimum of 1% and up to 10% or more) and a pressure of nearly 1,500 atm. We note that the observables here are real material changes in time, in contrast to those based on changes of optical/contrast intensity or diffraction.
Co-reporter:Hyun Soon Park, Oh-Hoon Kwon, J. Spencer Baskin, Brett Barwick and Ahmed H. Zewail
Nano Letters 2009 Volume 9(Issue 11) pp:3954-3962
Publication Date(Web):October 26, 2009
DOI:10.1021/nl9032704
The in situ martensitic phase transformation of iron, a complex solid-state transition involving collective atomic displacement and interface movement, is studied in real time by means of four-dimensional (4D) electron microscopy. The iron nanofilm specimen is heated at a maximum rate of ∼1011 K/s by a single heating pulse, and the evolution of the phase transformation from body-centered cubic to face-centered cubic crystal structure is followed by means of single-pulse, selected-area diffraction and real-space imaging. Two distinct components are revealed in the evolution of the crystal structure. The first, on the nanosecond time scale, is a direct martensitic transformation, which proceeds in regions heated into the temperature range of stability of the fcc phase, 1185−1667 K. The second, on the microsecond time scale, represents an indirect process for the hottest central zone of laser heating, where the temperature is initially above 1667 K and cooling is the rate-determining step. The mechanism of the direct transformation involves two steps, that of (barrier-crossing) nucleation on the reported nanosecond time scale, followed by a rapid grain growth typically in ∼100 ps for 10 nm crystallites.
Journal of the American Chemical Society 2009 Volume 131(Issue 44) pp:16010-16011
Publication Date(Web):October 20, 2009
DOI:10.1021/ja908079x
Microscopy imaging indicates that in situ carbon nanotubes (CNTs) irradiation with relatively low dosages of infrared radiation results in significant heating of the tubes to temperatures above 1300 K. Ultrafast temperature-jump experiments reveal that CNTs laser-induced heating and subsequent cooling in solution take tens and hundreds of picoseconds, respectively. Given the reported transient behavior, these observations suggest novel ways for a T-jump methodology, unhindered by the requirement for excitation of water in the study of biological structures. They also provide the rate information needed for optimization of photothermal therapy that invokes infrared irradiation to selectively heat and annihilate cancer cells.
Journal of the American Chemical Society 2009 Volume 131(Issue 50) pp:17998-18015
Publication Date(Web):November 30, 2009
DOI:10.1021/ja907432p
In this Perspective, 4D electron imaging is highlighted, after introducing some concepts, with an overview of selected applications that span chemical reactions, molecular interfaces, phase transitions, and nano(micro)mechanical systems. With the added dimension of time in microscopy, diffraction, and electron-energy-loss spectroscopy, the focus is on direct visualization of structural dynamics with atomic and nanoscale resolution in the four dimensions of space and time. This contribution provides an exposé of emerging developments and an outlook on future applications in materials and biological sciences.
Co-reporter:Milo M. Lin, Dmitry Shorokhov and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2009 vol. 11(Issue 45) pp:10619-10632
Publication Date(Web):15 Sep 2009
DOI:10.1039/B910794K
Of special interest in molecular biology is the study of structural and conformational changes which are free of the additional effects of the environment. In the present contribution, we report on the ultrafast unfolding dynamics of a large DNA macromolecular ensemble in vacuo for a number of temperature jumps, and make a comparison with the unfolding dynamics of the DNA in aqueous solution. A number of coarse-graining approaches, such as kinetic intermediate structure (KIS) model and ensemble-averaged radial distribution functions, are used to account for the transitional dynamics of the DNA without sacrificing the structural resolution. The studied ensembles of DNA macromolecules were generated using distributed molecular dynamics (MD) simulations, and the ensemble convergence was ensured by monitoring the ensemble-averaged radial distribution functions and KIS unfolding trajectories. Because the order–disorder transition in free DNA implies unzipping, coiling, and strand-separation processes which occur consecutively or competitively depending on the initial and final temperature of the ensemble, DNA order–disorder transition in vacuo cannot be described as a two-state (un)folding process.
Co-reporter:Fabrizio Carbone, Brett Barwick, Oh-Hoon Kwon, Hyun Soon Park, J. Spencer Baskin, Ahmed H. Zewail
Chemical Physics Letters 2009 Volume 468(4–6) pp:107-111
Publication Date(Web):22 January 2009
DOI:10.1016/j.cplett.2008.12.027
Electron energy loss spectroscopy (EELS) is a powerful tool in the study of valency, bonding and structure of solids. Previously, EEL spectra were either time-integrated or at best time-resolved on the millisecond to seconds scale, being limited by video rates and detector responses. Here, using our 4D electron microscope, we report ultrafast EELS, taking the time resolution in the energy–time space into the femtosecond regime, a 10 order of magnitude increase, and for a table-top apparatus. It is shown that the energy–time–amplitude space of graphite is selective to changes, especially in the electron density of the π + σ plasmon of the collective oscillation of the four electrons of carbon.3D time–energy–amplitude evolution of femtosecond resolved EEL spectra.
We consider here the extension of four-dimensional (4D) electron imaging methodology to the attosecond time domain. Specifically, we discuss the generation of attosecond electron pulses and the in situ probing with electron diffraction. The free electron pulses have a de Broglie wavelength on the order of picometers and a high degree of monochromaticity (ΔE/E0 ≈ 10−4); attosecond optical pulses have typically a wavelength of 20 nm and ΔE/E0 ≈ 0.5, where E0 is the central energy and ΔE is the energy bandwidth. Diffraction, and tilting of the electron pulses/specimen, permit the direct investigation of electron density changes in molecules and condensed matter. We predict the relevant changes in diffraction caused by electron density motion and give two examples as prototype applications, one that involves matter-field interaction, and the other is that of change in bonding order. This 4D imaging on the attosecond time scale is a pump–probe approach in free space and with free electrons.
Co-reporter:Brett Barwick,
David J. Flannigan
&
Ahmed H. Zewail
Nature 2009 462(7275) pp:902
Publication Date(Web):2009-12-17
DOI:10.1038/nature08662
Optical near-field microscopies can achieve spatial resolutions beyond the diffraction limit, but they cannot match the atomic-scale resolution of electron microscopy. Here, the development of photon-induced near-field electron microscopy — an ingenious blend of these two imaging modalities — opens the way for direct space-time imaging of localized fields at interfaces and visualization of phenomena related to photonics, plasmonics and nanostructures.
Interfacial water has unique properties in various functions. Here, using 4-dimensional (4D), ultrafast electron crystallography
with atomic-scale spatial and temporal resolution, we report study of structure and dynamics of interfacial water assembly
on a hydrophobic surface. Structurally, vertically stacked bilayers on highly oriented pyrolytic graphite surface were determined
to be ordered, contrary to the expectation that the strong hydrogen bonding of water on hydrophobic surfaces would dominate
with suppressed interfacial order. Because of its terrace morphology, graphite plays the role of a template. The dynamics
is also surprising. After the excitation of graphite by an ultrafast infrared pulse, the interfacial ice structure undergoes
nonequilibrium “phase transformation” identified in the hydrogen-bond network through the observation of structural isosbestic
point. We provide the time scales involved, the nature of ice-graphite structural dynamics, and relevance to properties related
to confined water.
Co-reporter:Shawn A. Hilbert;Herman Batelaan;Cornelis Uiterwaal;Brett Barwick
PNAS 2009 Volume 106 (Issue 26 ) pp:10558-10563
Publication Date(Web):2009-06-30
DOI:10.1073/pnas.0904912106
Here, we describe the “temporal lens” concept that can be used for the focus and magnification of ultrashort electron packets
in the time domain. The temporal lenses are created by appropriately synthesizing optical pulses that interact with electrons
through the ponderomotive force. With such an arrangement, a temporal lens equation with a form identical to that of conventional
light optics is derived. The analog of ray diagrams, but for electrons, are constructed to help the visualization of the process
of compressing electron packets. It is shown that such temporal lenses not only compensate for electron pulse broadening due
to velocity dispersion but also allow compression of the packets to durations much shorter than their initial widths. With
these capabilities, ultrafast electron diffraction and microscopy can be extended to new domains,and, just as importantly,
electron pulses can be delivered directly on an ultrafast techniques target specimen.
Co-reporter:Milo M. Lin, Dmitry Shorokhov and Ahmed H. Zewail
The Journal of Physical Chemistry A 2009 Volume 113(Issue 16) pp:4075-4093
Publication Date(Web):March 25, 2009
DOI:10.1021/jp8104425
In this article we consider consequences of spatial coherences and conformations in diffraction of (macro)molecules with different potential energy landscapes. The emphasis is on using this understanding to extract structural and temporal information from diffraction experiments. The theoretical analysis of structural interconversions spans an increased range of complexity, from small hydrocarbons to proteins. For each molecule considered, we construct the potential energy landscape and assess the characteristic conformational states available. For molecules that are quasiharmonic in the vicinity of energy minima, we find that the distinct conformer model is sufficient even at high temperatures. If, however, the energy surface is either locally flat around the minima or the molecule includes many degrees of conformational freedom, a Boltzmann ensemble must be used, in what we define as the pseudoconformer approach, to reproduce the diffraction. For macromolecules with numerous energy minima, the ensemble of hundreds of structures is considered, but we also utilize the concept of the persistence length to provide information on orientational coherence and its use to assess the degree of resonance contribution to diffraction. It is shown that the erosion of the resonant features in diffraction which are characteristic of some quasiperiodic structural motifs can be exploited in experimental studies of conformational interconversions triggered by a laser-induced temperature jump.
Co-reporter:Christina M. Othon;Oh-Hoon Kwon;Milo M. Lin;
Proceedings of the National Academy of Sciences 2009 106(31) pp:12593-12598
Publication Date(Web):July 21, 2009
DOI:10.1073/pnas.0905967106
Protein structural integrity and flexibility are intimately tied to solvation. Here, we examine the effect that changes in
bulk and local solvent properties have on protein structure and stability. We observe the change in solvation of an unfolding
of the protein model, melittin, in the presence of a denaturant, trifluoroethanol. The peptide system displays a well defined
transition in that the tetramer unfolds without disrupting the secondary or tertiary structure. In the absence of local structural
perturbation, we are able to reveal exclusively the role of solvation dynamics in protein structure stabilization and the
(un)folding pathway. A sudden retardation in solvent dynamics, which is coupled to the change in protein structure, is observed
at a critical trifluoroethanol concentration. The large amplitude conformational changes are regulated by the local solvent
hydrophobicity and bulk solvent viscosity.
In this contribution, we highlight the state of the art in the determination of structures with ultrafast electrons and X-rays. We provide our perspectives and reflections on the principles, techniques and methods, and on applications from different disciplines, with some focus on physical, chemical and biological structures. Although this article is not a survey of all the work done with these techniques, it provides a comprehensive referencing to current research.
Co-reporter:Hyun Soon Park, J. Spencer Baskin, Brett Barwick, Oh-Hoon Kwon, Ahmed H. Zewail
Ultramicroscopy 2009 Volume 110(Issue 1) pp:7-19
Publication Date(Web):December 2009
DOI:10.1016/j.ultramic.2009.08.005
In four-dimensional (4D) ultrafast electron microscopy (UEM), timed-pulse electron imaging and selected-area diffraction are used to study structural dynamics with space- and time-resolutions that allow direct observation of transformations affecting the fundamental properties of materials. Only recently, the UEM studies have begun to reveal a variety of dynamic responses of nanoscale specimens to material excitation, on ultrafast time scales and up to microseconds. Here, we give an account of some of these results, including imaging and diffraction dynamics of gold and graphite single crystal films, revealing atomic motions and morphology change in the former and two forms of acoustic resonance in the latter. We also report, for the first time, dynamic changes upon lattice excitation of moiré fringes in graphite, recorded in bright- and dark-field images. Oscillations that are seen in moiré fringe spacing and other selected-area image properties have the same temporal period as observed in Bragg spot changes in diffraction patterns from the same specimen areas. This period is shown to vary linearly with the local thickness of the specimen, thus establishing that the oscillations are due to excitation of a resonant elastic modulation of the film thickness and allowing derivation of a value of the Young's modulus (c33) of 36 GPa for the c-axis strain. The second form of resonance dynamics observed in graphite, on much longer time scales, corresponds to an out-of-plane drumming vibration of the film consistent with a 0.94 TPa elastic modulus for in-plane (a-axis) stretching. For the latter, the nanoscale membrane motion appears complicated (“chaotic”) at early time and builds up to a resonance at longer times. Finally, electron energy loss spectroscopy (EELS) in the UEM provides a unique domain of study of chemical bonding on the time scale of change (femtoseconds), and its application to graphite is discussed.
Co-reporter:Oh-Hoon Kwon, Brett Barwick, Hyun Soon Park, J. Spencer Baskin and Ahmed H. Zewail
Nano Letters 2008 Volume 8(Issue 11) pp:3557-3562
Publication Date(Web):November 12, 2008
DOI:10.1021/nl8029866
With four-dimensional (4D) electron microscopy, we report in situ imaging of the mechanical drumming of a nanoscale material. The single crystal graphite film is found to exhibit global resonance motion that is fully reversible and follows the same evolution after each initiating stress pulse. At early times, the motion appears “chaotic” showing the different mechanical modes present over the micron scale. At longer time, the motion of the thin film collapses into a well-defined fundamental frequency of 1.08 MHz, a behavior reminiscent of mode locking; the mechanical motion damps out after ∼200 μs and the oscillation has a “cavity” quality factor of 150. The resonance time is determined by the stiffness of the material, and for the 75 nm thick and 40 μm square specimen used here we determined Young’s modulus to be 1.0 TPa for the in-plane stress−strain profile. Because of its real-time dimension, this 4D microscopy should have applications in the study of these and other types of materials structures.
Co-reporter:Milo M. Lin, Lars Meinhold, Dmitry Shorokhov and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2008 vol. 10(Issue 29) pp:4227-4239
Publication Date(Web):03 Jun 2008
DOI:10.1039/B804675C
A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 μs predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.
Co-reporter:Andreas Gahlmann, Sang Tae Park and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2008 vol. 10(Issue 20) pp:2894-2909
Publication Date(Web):31 Mar 2008
DOI:10.1039/B802136H
Pulsed electron beams allow for the direct atomic-scale observation of structures with femtosecond to picosecond temporal resolution in a variety of fields ranging from materials science to chemistry and biology, and from the condensed phase to the gas phase. Motivated by recent developments in ultrafast electron diffraction and imaging techniques, we present here a comprehensive account of the fundamental processes involved in electron pulse propagation, and make comparisons with experimental results. The electron pulse, as an ensemble of charged particles, travels under the influence of the space–charge effect and the spread of the momenta among its electrons. The shape and size, as well as the trajectories of the individual electrons, may be altered. The resulting implications on the spatiotemporal resolution capabilities are discussed both for the N-electron pulse and for single-electron coherent packets introduced for microscopy without space–charge.
Physical Chemistry Chemical Physics 2008 vol. 10(Issue 20) pp:2879-2893
Publication Date(Web):01 Apr 2008
DOI:10.1039/B801626G
In this perspective we highlight developments and concepts in the field of 4D electron imaging. With spatial and temporal resolutions reaching the picometer and femtosecond, respectively, the field is now embracing ultrafast electron diffraction, crystallography and microscopy. Here, we overview the principles involved in the direct visualization of structural dynamics with applications in chemistry, materials science and biology. The examples include the studies of complex isolated chemical reactions, phase transitions and cellular structures. We conclude with an outlook on the potential of the approach and with some questions that may define new frontiers of research.
Chemical Physics Letters 2008 Volume 462(1–3) pp:14-17
Publication Date(Web):1 September 2008
DOI:10.1016/j.cplett.2008.07.072
Here, we report on the possible achievement, in ultrafast electron diffraction and imaging, of temporal resolution of tens of femtoseconds through the use of chirped electron packets in combination with energy filtering. Space–charge forces in multi-electron packets accelerate leading electrons and retard trailing ones, thus inducing correlations of momentum and time. By resolving the diffraction images with an energy analyzer, well-defined temporal slices of the long electron packet can be selected. Numerical simulations show that conventional electron sources are sufficient to reach the 30-fs domain of resolution without electron packet compression. They also reveal the influence of packet shape, electron density and photoemission bandwidth on the achievable time resolution.Thirty-famtosecond time resolution in ultrafast electron diffraction using a chirped electron packet and an energy filter.
In many physical and biological systems the transition from an amorphous to ordered native structure involves complex energy
landscapes, and understanding such transformations requires not only their thermodynamics but also the structural dynamics
during the process. Here, we extend our 4D visualization method with electron imaging to include the study of irreversible
processes with a single pulse in the same ultrafast electron microscope (UEM) as used before in the single-electron mode for
the study of reversible processes. With this augmentation, we report on the transformation of amorphous to crystalline structure
with silicon as an example. A single heating pulse was used to initiate crystallization from the amorphous phase while a single
packet of electrons imaged selectively in space the transformation as the structure continuously changes with time. From the
evolution of crystallinity in real time and the changes in morphology, for nanosecond and femtosecond pulse heating, we describe
two types of processes, one that occurs at early time and involves a nondiffusive motion and another that takes place on a
longer time scale. Similar mechanisms of two distinct time scales may perhaps be important in biomolecular folding.
The confined electronic structure of nanoscale materials has increasingly been shown to induce behavior quite distinct from that of bulk analogs. Direct atomic-scale visualization of nanowires of zinc oxide was achieved through their unique pancake-type diffraction by using four-dimensional (4D) ultrafast electron crystallography. After electronic excitation of this wide-gap photonic material, the wires were found to exhibit colossal expansions, two orders of magnitude higher than that expected at thermal equilibrium; the expansion is highly anisotropic, a quasi–one-dimensional behavior, and is facilitated by the induced antibonding character. By reducing the density of nanowires, the expansions reach even larger values and occur at shorter times, suggesting a decrease of the structural constraint in transient atomic motions. This unanticipated ultrafast carrier-driven expansion highlights the optoelectronic consequences of nanoscale morphologies.
Two centuries ago solvated electrons were discovered in liquid ammonia and a century later the concept of the solvent cage was introduced. Here, we report a real time study of the dynamics of size-selected clusters, n=20 to 60, of electrons in ammonia, and, for comparison, that of electrons in water cages. Unlike the water case, the observed dynamics for ammonia indicates the formation, through a 100 fs temperature jump, of a solvent collective motion in a 500 fs relaxation process. The agreement of the experimental results—obtained for a well-defined n, gated electron kinetic energy, and time delay—with molecular dynamics theory suggests the critical and different role of the kinetic energy and the librational motions involved in solvation.
With advances in spatial resolution reaching the atomic scale, two-dimensional (2D) and 3D imaging in electron microscopy has become an essential methodology in various fields of study. Here, we report 4D imaging, with in situ spatiotemporal resolutions, in ultrafast electron microscopy (UEM). The ability to capture selected-area-image dynamics with pixel resolution and to control the time separation between pulses for temporal cooling of the specimen made possible studies of fleeting structures and morphologies. We demonstrate the potential for applications with two examples, gold and graphite. For gold, after thermally induced stress, we determined the atomic structural expansion, the nonthermal lattice temperature, and the ultrafast transients of warping/bulging. In contrast, in graphite, striking coherent transients of the structure were observed in both image and diffraction, directly measuring, on the nanoscale, the longitudinal resonance period governed by Young's elastic modulus. The success of these studies demonstrates the promise of UEM in real-space imaging of dynamics.
The mechanism of electron pairing in high-temperature superconductors is still the subject of intense debate. Here, we provide
direct evidence of the role of structural dynamics, with selective atomic motions (buckling of copper–oxygen planes), in the
anisotropic electron-lattice coupling. The transient structures were determined using time-resolved electron diffraction,
following carrier excitation with polarized femtosecond heating pulses, and examined for different dopings and temperatures.
The deformation amplitude reaches 0.5% of the c axis value of 30 Å when the light polarization is in the direction of the copper–oxygen bond, but its decay slows down at
45°. These findings suggest a selective dynamical lattice involvement with the anisotropic electron–phonon coupling being
on a time scale (1–3.5 ps depending on direction) of the same order of magnitude as that of the spin exchange of electron
pairing in the high-temperature superconducting phase.
The fluorescence decays of several analogues of the photoactive yellow protein (PYP) chromophore in aqueous solution have been measured by femtosecond fluorescence up-conversion and the corresponding time-resolved fluorescence spectra have been reconstructed. The native chromophore of PYP is a thioester derivative of p-coumaric acid in its trans deprotonated form. Fluorescence kinetics are reported for a thioester phenyl analogue and for two analogues where the thioester group has been changed to amide and carboxylate groups. The kinetics are compared to those we previously reported for the analogues bearing ketone and ester groups. The fluorescence decays of the full series are found to lie in the 1–10 ps range depending on the electron-acceptor character of the substituent, in good agreement with the excited-state relaxation kinetics extracted from transient absorption measurements. Steady-state photolysis is also examined and found to depend strongly on the nature of the substituent. While it has been shown that the ultrafast light-induced response of the chromophore in PYP is controlled by the properties of the protein nanospace, the present results demonstrate that, in solution, the relaxation dynamics and pathway of the chromophore is controlled by its electron donor–acceptor structure: structures of stronger electron donor–acceptor character lead to faster decays and less photoisomerisation.
Complex systems in condensed phases involve a multidimensional energy landscape, and knowledge of transitional structures and separation of time scales for atomic movements is critical to understanding their dynamical behavior. Here, we report, using four-dimensional (4D) femtosecond electron diffraction, the visualization of transitional structures from the initial monoclinic to the final tetragonal phase in crystalline vanadium dioxide; the change was initiated by a near-infrared excitation. By revealing the spatiotemporal behavior from all observed Bragg diffractions in 3D, the femtosecond primary vanadium–vanadium bond dilation, the displacements of atoms in picoseconds, and the sound wave shear motion on hundreds of picoseconds were resolved, elucidating the nature of the structural pathways and the nonconcerted mechanism of the transformation.
In this contribution, we consider the advancement of ultrafast electron diffraction and microscopy to cover the attosecond
time domain. The concept is centered on the compression of femtosecond electron packets to trains of 15-attosecond pulses
by the use of the ponderomotive force in synthesized gratings of optical fields. Such attosecond electron pulses are significantly
shorter than those achievable with extreme UV light sources near 25 nm (≈50 eV) and have the potential for applications in
the visualization of ultrafast electron dynamics, especially of atomic structures, clusters of atoms, and some materials.
Co-reporter:Lars Meinhold;Jeremy C. Smith;Akio Kitao
PNAS 2007 Volume 104 (Issue 44 ) pp:17261-17265
Publication Date(Web):2007-10-30
DOI:10.1073/pnas.0708199104
Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein
energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of
temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating
that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast,
vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the
atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency
collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e.,
the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an
invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions
in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation.
We report real-time observations of the folding and melting of DNA by probing two active sites of a hairpin structure, the
bases and the stem end, and using an ultrafast T-jump. Studies at different initial temperatures (before, during, and after melting) provide the time scale of water heating
(<20 ps), single-strand destacking (700 ps to 2 ns), and hairpin destacking (microseconds and longer) in solutions of various
ionic strengths and pH values. The behavior of transient changes gives direct evidence to the existence of intermediate collapsed
structures, labile in destacking but compact in nature, and indicates that melting is not a two-state process. We propose
a landscape that is defined by these nucleation structures and destacking for efficient folding and melting.
Co-reporter:David J. Flannigan Dr.;Vladimir A. Lobastov Dr.;Ahmed H. Zewail Dr.
Angewandte Chemie 2007 Volume 119(Issue 48) pp:
Publication Date(Web):5 DEC 2007
DOI:10.1002/ange.200790245
Ultraschnelle Elektronenmikroskopie …… visualisiert das durch Nah-IR-Laserpulse induzierte, reversible Ausdehnen und Zusammenziehen eines [Cu(TCNQ)]-Einkristalls (siehe Bildfolge; TCNQ=7,7,8,8-Tetracyanchinodimethan) sowie die photochemische Reduktion der Kupferionen unter Bildung diskreter Metallcluster (oben rechts), wie A. H. Zewail et al. in der Zuschrift auf S. 9366 ff. schildern. Der Kristall dehnt sich unter Bestrahlung entlang der π-Stapelachse der TCNQ-Moleküle aus und kehrt nach dem Abschalten des Lasers in die Ausgangsstruktur zurück.
Co-reporter:David J. Flannigan Dr.;Vladimir A. Lobastov Dr.;Ahmed H. Zewail Dr.
Angewandte Chemie 2007 Volume 119(Issue 48) pp:
Publication Date(Web):6 NOV 2007
DOI:10.1002/ange.200704147
Hin und her: Das reversible Ausdehnen und Zusammenziehen eines [Cu(TCNQ)]-Einkristalls kann durch einen Nahinfrarot-Laserpuls ausgelöst und durch ultraschnelle Elektronenmikroskopie verfolgt werden (TCNQ = 7,7,8,8-Tetracyanchinodimethan). Unter Bestrahlung dehnt sich der Kristall entlang der π-Stapelachse der TCNQ-Moleküle aus, nicht aber senkrecht zu dieser. Nach dem Abschalten des Lasers kehrt der Kristall in die Ausgangsstruktur zurück.
Nonequilibrium phase transitions, which are defined by the formation of macroscopic transient domains, are optically dark and cannot be observed through conventional temperature- or pressure-change studies. We have directly determined the structural dynamics of such a nonequilibrium phase transition in a cuprate superconductor. Ultrafast electron crystallography with the use of a tilted optical geometry technique afforded the necessary atomic-scale spatial and temporal resolutions. The observed transient behavior displays a notable “structural isosbestic” point and a threshold effect for the dependence of c-axis expansion (Δc) on fluence (F), with Δc/F = 0.02 angstrom/(millijoule per square centimeter). This threshold for photon doping occurs at ∼0.12 photons per copper site, which is unexpectedly close to the density (per site) of chemically doped carriers needed to induce superconductivity.
Co-reporter:David J. Flannigan Dr.;Vladimir A. Lobastov Dr.;Ahmed H. Zewail Dr.
Angewandte Chemie International Edition 2007 Volume 46(Issue 48) pp:
Publication Date(Web):5 DEC 2007
DOI:10.1002/anie.200790245
Ultrafast electron microscopy …… has been used to view the reversible expansion and contraction of a single crystal of [Cu(TCNQ)] (see film strip; TCNQ=7,7,8,8-tetracyanoquinodimethane), induced with near-infrared laser pulses, as well as the photoinduced reduction of copper ions to form discrete metal clusters (see picture, top right), as described by A. H. Zewail et al. in their Communication on Page 9206 ff. The crystal expands along the π-stacking axis of the TCNQ molecules upon exposure to light, but rapidly returns to its original state in the absence of laser light.
Co-reporter:David J. Flannigan Dr.;Vladimir A. Lobastov Dr.;Ahmed H. Zewail Dr.
Angewandte Chemie International Edition 2007 Volume 46(Issue 48) pp:
Publication Date(Web):6 NOV 2007
DOI:10.1002/anie.200704147
On again, off again: The reversible expansion and contraction of single crystals of [Cu(TCNQ)] induced by near-infrared laser pulses was studied with ultrafast electron microscopy (TCNQ=7,7,8,8-tetracyanoquinodimethane). The crystal expands along the π-stacking axis of the TCNQ molecules, but not perpendicular to this axis, when exposed to light. The crystal returned to its original structure when the laser light was blocked.
The dynamics of excited-state double proton transfer of model DNA base pairs, 7-azaindole dimers, is reported using femtosecond
fluorescence spectroscopy. To elucidate the nature of the transfer in the condensed phase, here we examine variation of solvent
polarity and viscosity, solute concentration, and isotopic fractionation. The rate of proton transfer is found to be significantly
dependent on polarity and on the isotopic composition in the pair. Consistent with a stepwise mechanism, the results support
the presence of an ionic intermediate species which forms on the femtosecond time scale and decays to the final tautomeric
form on the picosecond time scale. We discuss the results in relation to the molecular motions involved and comment on recent
claims of concerted transfer in the condensed phase. The nonconcerted mechanism is in agreement with previous isolated-molecule
femtosecond dynamics and is also consistent with the most-recent high-level theoretical study on the same pair.
Co-reporter:Oliviero Andreussi, Davide Donadio, Michele Parrinello, Ahmed H. Zewail
Chemical Physics Letters 2006 Volume 426(1–3) pp:115-119
Publication Date(Web):26 July 2006
DOI:10.1016/j.cplett.2006.04.114
Stimulated by recent experiments [C.-Y. Ruan et al. Science 304, (2004) 81], we have performed molecular dynamics and ab initio structural studies of the laser-induced heating and restructuring processes of nanometer-scale ice on a substrate of chlorine terminated Si(1 1 1). Starting from proton disordered cubic ice configurations the thin film behavior has been characterized at several temperatures up to the melting point. The surface induces order with crystallization in the Ic lattice, but with void amorphous regions. The structure changes on the ultrashort time scale and restructures by heat dissipation depending on the relaxation time and final temperature. Our results show the general behavior observed experimentally, thus providing the nature of forces in the atomic-scale description of interfacial ice.Stimulated by ultrafast electron crystallography experiments, here reported are molecular dynamics and ab initio structural studies of the laser-induced heating and restructuring processes of nanometer-scale ice on a substrate of chlorine terminated Si(1 1 1). The results show the general behavior observed experimentally, thus providing the nature of forces in the atomic-scale description of interfacial ice.
Struktur und Dynamik von Mono- und Doppelschicht-Phospholipiden (siehe Bild) wurden mithilfe ultraschneller Elektronenkristallographie räumlich-zeitlich aufgelöst. Nach einem Femtosekunden-Temperatursprung im Substrat wurden die Ausdehnung und Restrukturierung der Ketten beobachtet und dabei eine transiente strukturelle Ordnung erkannt. Die atomaren Kräfte wurden im Nichtgleichgewichtszustand des Systems als kohärent identifiziert.
Angewandte Chemie International Edition 2006 Volume 45(Issue 31) pp:
Publication Date(Web):31 JUL 2006
DOI:10.1002/anie.200601778
The structure and dynamics of monolayer and bilayer (see picture) phospholipids have been studied with spatiotemporal resolutions by ultrafast electron crystallography. The expansion and restructuring of the chains were observed after a femtosecond temperature jump in the substrate, and a transient structural ordering was revealed. The atomic forces were identified to be coherent in the non-equilibrium state of the assembly.
Ultrafast electron microscopy and diffraction are powerful techniques for the study of the time-resolved structures of molecules,
materials, and biological systems. Central to these approaches is the use of ultrafast coherent electron packets. The electron
pulses typically have an energy of 30 keV for diffraction and 100–200 keV for microscopy, corresponding to speeds of 33–70%
of the speed of light. Although the spatial resolution can reach the atomic scale, the temporal resolution is limited by the
pulse width and by the difference in group velocities of electrons and the light used to initiate the dynamical change. In
this contribution, we introduce the concept of tilted optical pulses into diffraction and imaging techniques and demonstrate
the methodology experimentally. These advances allow us to reach limits of time resolution down to regimes of a few femtoseconds
and, possibly, attoseconds. With tilted pulses, every part of the sample is excited at precisely the same time as when the
electrons arrive at the specimen. Here, this approach is demonstrated for the most unfavorable case of ultrafast crystallography.
We also present a method for measuring the duration of electron packets by autocorrelating electron pulses in free space and
without streaking, and we discuss the potential of tilting the electron pulses themselves for applications in domains involving
nuclear and electron motions.
Between isolated atoms or molecules and bulk materials there lies a class of unique structures, known as clusters, that consist
of a few to hundreds of atoms or molecules. Within this range of “nanophase,” many physical and chemical properties of the
materials evolve as a function of cluster size, and materials may exhibit novel properties due to quantum confinement effects.
Understanding these phenomena is in its own rights fundamental, but clusters have the additional advantage of being controllable
model systems for unraveling the complexity of condensed-phase and biological structures, not to mention their vanguard role
in defining nanoscience and nanotechnology. Over the last two decades, much progress has been made, and this short overview
highlights our own involvement in developing cluster dynamics, from the first experiments on elementary systems to model systems
in the condensed phase, and on to biological structures.
The cycle of the photoactive yellow protein (PYP) has been extensively studied, but the dynamics of the isolated chromophore
responsible for transduction is unknown. Here, we present real-time observation of the dynamics of the negatively charged
chromophore and detection of intermediates along the path of trans-to-cis isomerization using femtosecond mass selection/electron
detachment techniques. The results show that the role of the protein environment is not in the first step of double-bond twisting
(barrier crossing) but in directing efficient conversion to the cis-structure and in impeding radical formation within the
protein.
A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.
Electron scattering expressions are presented which are applicable to very general conditions of implementation of anisotropic ultrafast electron diffraction (UED) experiments on the femto- and picosecond time scale. “Magic angle” methods for extracting from the experimental diffraction patterns both the isotropic scalar contribution (population dynamics) and the angular (orientation-dependent) contribution are described. To achieve this result, the molecular scattering intensity is given as an expansion in terms of the moments of the transition-dipole distribution created by the linearly polarized excitation laser pulse. The isotropic component (n=0 moment) depends only on population and scalar internuclear separations, and the higher moments reflect bond angles and evolve in time due to rotational motion of the molecules. This clear analytical separation facilitates assessment of the role of experimental variables in determining the influence of anisotropic orientational distributions of the molecular ensembles on the measured diffraction patterns. Practical procedures to separate the isotropic and anisotropic components of experimental data are evaluated and demonstrated with application to reactions. The influence of vectorial properties (bond angles and rotational dynamics) on the anisotropic component adds a new dimension to UED, arising through the imposition of spatial order on otherwise randomly oriented ensembles.
Co-reporter:Agathe Espagne Dr.;Daniel H. Paik Dr. ;Pascale Changenet-Barret Dr.;Monique M. Martin
ChemPhysChem 2006 Volume 7(Issue 8) pp:1717-1726
Publication Date(Web):17 JUL 2006
DOI:10.1002/cphc.200600137
We investigate solvent viscosity and polarity effects on the photoisomerization of the protonated and deprotonated forms of two analogues of the photoactive yellow protein (PYP) chromophore. These are trans-p-hydroxybenzylidene acetone and trans-p-hydroxyphenyl cinnamate, studied in solutions of different polarity and viscosity at room temperature, by means of femtosecond fluorescence up-conversion. The fluorescence lifetimes of the protonated forms are found to be barely sensitive to solvent viscosity, and to increase with increasing solvent polarity. In contrast, the fluorescence decays of the deprotonated forms are significantly slowed down in viscous media and accelerated in polar solvents. These results elucidate the dramatic influence of the protonation state of the PYP chromophore analogues on their photoinduced dynamics. The viscosity and polarity effects are, respectively, interpreted in terms of different isomerization coordinates and charge redistribution in S1. A trans-to-cis isomerization mechanism involving mainly the ethylenic double-bond torsion and/or solvation is proposed for the anionic forms, whereas “concerted” intramolecular motions are proposed for the neutral forms.
Co-reporter:Yonggang He;Andreas Gahlmann;Jonathan S. Feenstra;Sang Tae Park;Ahmed H. Zewail
Chemistry – An Asian Journal 2006 Volume 1(Issue 1-2) pp:
Publication Date(Web):3 JUL 2006
DOI:10.1002/asia.200600107
Nitro compounds release NO, NO2, and other species, but neither the structures during the reactions nor the time scales are known. Ultrafast electron diffraction (UED) allowed the study of the NO release from nitrobenzene, and the molecular pathways and the structures of the transient species were identified. It was observed, in contrast to previous inferences, that nitric oxide and phenoxyl radicals are formed dominantly and that the time scale of formation is 8.8±2.2 ps. The structure of the phenoxyl radical was determined for the first time, and found to be quinoid-like. The mechanism proposed involves a repulsive triplet state, following intramolecular rearrangement. This efficient generation of NO may have important implications for the control of by-products in drug delivery and other applications.
Co-reporter:Ramesh Srinivasan;Jonathan S. Feenstra;Sang Tae Park;Shoujun Xu
Science 2005 Vol 307(5709) pp:558-563
Publication Date(Web):28 Jan 2005
DOI:10.1126/science.1107291
Abstract
The intermediate structures formed through radiationless transitions are termed “dark” because their existence is inferred indirectly from radiative transitions. We used ultrafast electron diffraction to directly determine these transient structures on both ground-state and excited-state potential energy surfaces of several aromatic molecules. The resolution in space and time (0.01 angstrom and 1 picosecond) enables differentiation between competing nonradiative pathways of bond breaking, vibronic coupling, and spin transition. For the systems reported here, the results reveal unexpected dynamical behavior. The observed ring opening of the structure depends on molecular substituents. This, together with the parallel bifurcation into physical and chemical channels, redefines structural dynamics of the energy landscape in radiationless processes.
Co-reporter:Tianbing Xia;Chaozhi Wan;Richard W. Roberts
PNAS 2005 102 (37 ) pp:13013-13018
Publication Date(Web):2005-09-13
DOI:10.1073/pnas.0506181102
The transcription antiterminator N protein from bacteriophage λ uses its arginine-rich motif to specifically bind a stem-loop
RNA hairpin (boxB) as a bent α-helix. A single stacking interaction between a tryptophan (Trp-18) and an adenosine (A7) in the RNA loop is
robust and necessary for antitermination activity in vivo. Previously, femtosecond fluorescence up-conversion experiments from this laboratory indicated that the N/boxB complex exists in a dynamical two-state equilibrium between stacked and unstacked conformations and that the extent of stacking
depends on the identity of peptide residues 14 and 15. In the present work, we have combined transient absorption and fluorescence
up-conversion to determine the nature of interactions responsible for this sequence-dependent behavior. Analysis of mutant
complexes supports the idea that the β-carbon of residue 14 enforces the stacked geometry by hydrophobic interaction with
the ribose of A7, whereas a positive charge at this residue plays only a secondary role. A positive charge at position 15
substantially disfavors the stacked state but retains much of the binding energy. Remarkably, in vivo antitermination experiments show strong correlation with our femtosecond dynamics, demonstrating how conformational interplay
can control the activity of a macromolecular machine.
Co-reporter:Tianbing Xia;Chaozhi Wan;Richard W. Roberts
PNAS 2005 102 (37 ) pp:13013-13018
Publication Date(Web):2005-09-13
DOI:10.1073/pnas.0506181102
The transcription antiterminator N protein from bacteriophage λ uses its arginine-rich motif to specifically bind a stem-loop
RNA hairpin (boxB) as a bent α-helix. A single stacking interaction between a tryptophan (Trp-18) and an adenosine (A7) in the RNA loop is
robust and necessary for antitermination activity in vivo. Previously, femtosecond fluorescence up-conversion experiments from this laboratory indicated that the N/boxB complex exists in a dynamical two-state equilibrium between stacked and unstacked conformations and that the extent of stacking
depends on the identity of peptide residues 14 and 15. In the present work, we have combined transient absorption and fluorescence
up-conversion to determine the nature of interactions responsible for this sequence-dependent behavior. Analysis of mutant
complexes supports the idea that the β-carbon of residue 14 enforces the stacked geometry by hydrophobic interaction with
the ribose of A7, whereas a positive charge at this residue plays only a secondary role. A positive charge at position 15
substantially disfavors the stacked state but retains much of the binding energy. Remarkably, in vivo antitermination experiments show strong correlation with our femtosecond dynamics, demonstrating how conformational interplay
can control the activity of a macromolecular machine.
The structure and dynamics of a biological model bilayer are reported with atomic-scale resolution by using ultrafast electron
crystallography. The bilayer was deposited as a Langmuir-Blodgett structure of arachidic (eicosanoic) fatty acids with the
two chains containing 40 carbon atoms (≈50 Å), on a hydrophobic substrate, the hydrogen terminated silicon(111) surface. We
determined the structure of the 2D assembly, establishing the orientation of the chains and the subunit cell of the CH2 distances: a
0 = 4.7 Å, b
0 = 8.0 Å, and c
0 = 2.54 Å. For structural dynamics, the diffraction frames were taken every 1 picosecond after a femtosecond temperature jump.
The observed motions, with sub-Å resolution and monolayer sensitivity, clearly indicate the coherent anisotropic expansion
of the bilayer solely along the aliphatic chains, followed by nonequilibrium contraction and restructuring at longer times.
This motion is indicative of a nonlinear behavior among the anharmonically coupled bonds on the ultrashort time scale and
energy redistribution and diffusion on the longer time scale. The ability to observe such atomic motions of complex structures
and at interfaces is a significant leap forward for the determination of macromolecular dynamical structures by using ultrafast
electron crystallography.
The structure and dynamics of a biological model bilayer are reported with atomic-scale resolution by using ultrafast electron
crystallography. The bilayer was deposited as a Langmuir-Blodgett structure of arachidic (eicosanoic) fatty acids with the
two chains containing 40 carbon atoms (≈50 Å), on a hydrophobic substrate, the hydrogen terminated silicon(111) surface. We
determined the structure of the 2D assembly, establishing the orientation of the chains and the subunit cell of the CH2 distances: a
0 = 4.7 Å, b
0 = 8.0 Å, and c
0 = 2.54 Å. For structural dynamics, the diffraction frames were taken every 1 picosecond after a femtosecond temperature jump.
The observed motions, with sub-Å resolution and monolayer sensitivity, clearly indicate the coherent anisotropic expansion
of the bilayer solely along the aliphatic chains, followed by nonequilibrium contraction and restructuring at longer times.
This motion is indicative of a nonlinear behavior among the anharmonically coupled bonds on the ultrashort time scale and
energy redistribution and diffusion on the longer time scale. The ability to observe such atomic motions of complex structures
and at interfaces is a significant leap forward for the determination of macromolecular dynamical structures by using ultrafast
electron crystallography.
Co-reporter:Dmitry Shorokhov Dr.;Sang Tae Park Dr. Dr.
ChemPhysChem 2005 Volume 6(Issue 11) pp:
Publication Date(Web):7 NOV 2005
DOI:10.1002/cphc.200500330
In this contribution, we report studies in ultrafast electron diffraction (UED), with the aim of exploring new directions. The main focus is on the determination of complex structures and their dynamics with spatial and temporal resolutions sufficient to give an atomic-scale picture for the evolution in chemical or biological change. We also provide the theoretical framework for UED, and compare the experimental findings of UED to those predicted by density functional and charge density calculations. Selected applications are given in order to highlight phenomena related to concepts such as bifurcation of trajectories in dynamics, far-from-equilibrium coherent structures, and conformational robustness in biological structures. For the former two cases, we consider chemical systems, and, for the latter, we examine proteins of 200 atoms (angiotensin I) or more.
The technique of ultrafast electron diffraction allows direct measurement of changes which occur in the molecular structures of isolated molecules upon excitation by femtosecond laser pulses. The vectorial nature of the molecule–radiation interaction also ensures that the orientation of the transient populations created by the laser excitation is not isotropic. Here, we examine the influence on electron diffraction measurements—on the femtosecond and picosecond timescales—of this induced initial anisotropy and subsequent inertial (collision-free) molecular reorientation, accounting for the geometry and dynamics of a laser-induced reaction (dissociation). The orientations of both the residual ground-state population and the excited- or product-state populations evolve in time, with different characteristic rotational dephasing and recurrence times due to differing moments of inertia. This purely orientational evolution imposes a corresponding evolution on the electron scattering pattern, which we show may be similar to evolution due to intrinsic structural changes in the molecule, and thus potentially subject to misinterpretation. The contribution of each internuclear separation is shown to depend on its orientation in the molecular frame relative to the transition dipole for the photoexcitation; thus not only bond lengths, but also bond angles leave a characteristic imprint on the diffraction. Of particular note is the fact that the influence of anisotropy persists at all times, producing distinct differences between the asymptotic “static” diffraction image and the predictions of isotropic diffraction theory.
Co-reporter:Chong-Yu Ruan;Vladimir A. Lobastov;Franco Vigliotti;Songye Chen
Science 2004 Vol 304(5667) pp:80-84
Publication Date(Web):02 Apr 2004
DOI:10.1126/science.1094818
Abstract
We report direct determination of the structures and dynamics of interfacial water on a hydrophilic surface with atomic-scale resolution using ultrafast electron crystallography. On the nanometer scale, we observed the coexistence of ordered surface water and crystallite-like ice structures, evident in the superposition of Bragg spots and Debye-Scherrer rings. The structures were determined to be dominantly cubic, but each undergoes different dynamics after the ultrafast substrate temperature jump. From changes in local bond distances (OH··O and O···O) with time, we elucidated the structural changes in the far-from-equilibrium regime at short times and near-equilibration at long times.
We directly observed the hydration dynamics of an excess electron in the finite-sized water clusters of with n = 15, 20, 25, 30, and 35. We initiated the solvent motion by exciting the hydrated electron in the cluster. By resolving the binding energy of the excess electron in real time with femtosecond resolution, we captured the ultrafast dynamics of the electron in the presolvated (“wet”) and hydrated states and obtained, as a function of cluster size, the subsequent relaxation times. The solvation time (300 femtoseconds) after the internal conversion [140 femtoseconds for ] was similar to that of bulk water, indicating the dominant role of the local water structure in the dynamics of hydration. In contrast, the relaxation in other nuclear coordinates was on a much longer time scale (2 to 10 picoseconds) and depended critically on cluster size.
Co-reporter:Franco Vigliotti Dr.;Songye Chen;Chong-Yu Ruan Dr.;Vladimir A. Lobastov Dr. Dr.
Angewandte Chemie International Edition 2004 Volume 43(Issue 20) pp:
Publication Date(Web):23 MAR 2004
DOI:10.1002/anie.200453983
A formidable contender to X-ray diffraction is ultrafast electron crystallography. Whereas the former is more suited to investigate the bulk of the substrate, the time, length, and sensitivity scales of electron crystallography provide powerful and complementary information on atomic-scale structural dynamics at the surface (see diffraction image of GaAs crystal).
Co-reporter:D. Hern Paik;Ding-Shyue Yang;I-Ren Lee Dr.
Angewandte Chemie 2004 Volume 116(Issue 21) pp:
Publication Date(Web):28 APR 2004
DOI:10.1002/ange.200453962
Ein Klassiker der physikalisch-organischen Chemie, die Inversion von Cyclooctatetraen (COT), wurde mit Femtosekundenauflösung durch Negativionenstrahl-Techniken untersucht. Der Übergangszustand der thermischen Inversion wurde durch Ablösung des Elektrons vom planaren COT−-Ion direkt erreicht (siehe Diagramm).
Co-reporter:Franco Vigliotti Dr.;Songye Chen;Chong-Yu Ruan Dr.;Vladimir A. Lobastov Dr. Dr.
Angewandte Chemie 2004 Volume 116(Issue 20) pp:
Publication Date(Web):5 MAY 2004
DOI:10.1002/ange.200490059
Die Dynamik von Oberflächenstrukturen wird mit präzedenzloser räumlicher und zeitlicher Auflösung durch ultraschnelle Elektronenkristallographie bestimmt. Die dynamischen Prozesse werden durch einen Femtosekunden-Laserpuls ausgelöst, ein ultrakurzer Elektronenpuls bildet die kurzlebigen Oberflächenstrukturen ab. Momentaufnahmen der Beugungsmuster zu Verzögerungszeiten Δt ermöglichen die Beobachtung der Dynamik von Oberflächenstrukturen in Echtzeit mit atomarer Auflösung. Mehr dazu erfahren Sie in der Zuschrift von A. H. Zewail et al. auf S. 2759 ff.
Co-reporter:Franco Vigliotti Dr.;Songye Chen;Chong-Yu Ruan Dr.;Vladimir A. Lobastov Dr. Dr.
Angewandte Chemie 2004 Volume 116(Issue 20) pp:
Publication Date(Web):23 MAR 2004
DOI:10.1002/ange.200453983
Ein würdiger Mitstreiter der Röntgenbeugung ist die ultraschnelle Elektronenkristallographie. Während sich die Röntgenbeugung besser für Untersuchungen der Volumenphase eignet, liefern die Zeit-, Längen- und Empfindlichkeitskalen der Elektronenkristallographie umfassende und komplementäre Informationen über dynamische Prozesse auf Oberflächen in atomarer Auflösung (siehe Beugungsbild eines GaAs-Kristalls).
Co-reporter:Liang Zhao;Samir Kumar Pal;Tianbing Xia Dr.
Angewandte Chemie 2004 Volume 116(Issue 1) pp:
Publication Date(Web):8 DEC 2003
DOI:10.1002/ange.200352961
Gut geschmiert: Wassermoleküle zwischen einem Protein (z. B. der bovinen Pankreas-Phospholipase A2) und einem micellaren Substrat wirken als Schmiermittel und erleichtern so die Bewegung und Bindung der Proteine auf der Oberfläche (siehe Bild). Untersuchungen der Hydratationsdynamik vor und nach der Komplexierung brachten zum Vorschein, dass diese Wechselwirkungen essenziell für die Funktion des Enzyms sind.
We report studies of unfolding and ultrafast hydration dynamics of the protein human serum albumin. Unique in this study is
our ability to examine different domains of the same protein and the intermediate on the way to the unfolded state. With femtosecond
resolution and site-selective labeling, we isolate the dynamics of domains I and II of the native protein, domain I of the
intermediate at 2 M guanidine hydrochloride, and the unfolded state at 6 M of the denaturant. For studies of unfolding, we
used the fluorophores, acrylodan (covalently bound to Cys-34 in domain I) and the intrinsic tryptophan (domain II), whereas
for hydration dynamics, we probed acrylodan and prodan; the latter is bound to domain II. From the time-dependent spectra
and the correlation functions, we obtained the time scale of dynamically ordered water: 57 ps for the more stable domain I
and 32 ps for the less stable domain II, in contrast to ≈0.8 ps for labile, bulk-type water. This trend suggests an increased
hydrophilic residues–water interaction of domain I, contrary to some packing models. In the intermediate state, which is characterized
by essentially intact domain I and unfolded domain II, the dynamics of ordered water around domain I is nearly the same (61
ps) as that of native state (57 ps), whereas that in the unfolded protein is much shorter (13 ps). We discuss the role of
this fluidity in the correlation between stability and function of the protein.
Co-reporter:D. Hern Paik;Ding-Shyue Yang;I-Ren Lee Dr.
Angewandte Chemie International Edition 2004 Volume 43(Issue 21) pp:
Publication Date(Web):28 APR 2004
DOI:10.1002/anie.200453962
A classic in physical organic chemistry, the inversion of cyclooctatetraene (COT), was studied with femtosecond resolution by negative-ion-beam techniques. The transition state for the thermal inversion was accessed directly by detachment of the electron from the planar COT− ion.
Femtosecond to nanosecond dynamics of O2 rebinding to human WT myoglobin and its mutants, V68F and I107F, have been studied by using transient absorption. The results
are compared with NO rebinding. Even though the immediate environment around the heme binding site is changed by the mutations,
the picosecond geminate rebinding of oxygen is at most minimally affected. On the other hand, the V68F (E11) mutation causes
drastic differences in rebinding on the nanosecond time scale, whereas the effect of the I107F (G8) mutation remains relatively
small within our 10-ns time window. Unlike traditional homogeneous kinetics and molecular dynamics collisional simulations,
we propose a “bifurcation model” for populations of directed and undirected dynamics on the ultrafast time scale, reflecting
the distribution of initial protein conformations. The major mutation effect occurs on the time scale on which global protein
conformational change is possible, consistent with transitions between the conformations of directed and undirected population
playing a role in the O2 binding. We discuss the relevance of these findings to the bimolecular function of the protein.
Co-reporter:Liang Zhao;Samir Kumar Pal;Tianbing Xia Dr.
Angewandte Chemie International Edition 2004 Volume 43(Issue 1) pp:
Publication Date(Web):8 DEC 2003
DOI:10.1002/anie.200352961
Slippery when wet: Water molecules at the interface between a protein (e.g. bovine pancreatic phospholipase A2) and a micellar substrate act as a lubricant and facilitate movement and binding of the protein at the surface (see picture). Studies of the hydration dynamics before and after complexation reveal that these interactions are crucial for enzymatic function.
With properly timed sequences of ultrafast electron pulses, it is now possible to image complex molecular structures in the four dimensions of space and time with resolutions of 0.01 Å and 1 ps, respectively. The new limits of ultrafast electron diffraction (UED) provide the means for the determination of transient molecular structures, including reactive intermediates and non-equilibrium structures of complex energy landscapes. By freezing structures on the ultrafast timescale, we are able to develop concepts that correlate structure with dynamics. Examples include structure-driven radiationless processes, dynamics-driven reaction stereochemistry, pseudorotary transition-state structures, and non-equilibrium structures exhibiting negative temperature, bifurcation, or selective energy localization in bonds. These successes in the studies of complex molecular systems, even without heavy atoms, and the recent development of a new machine devoted to structures in the condensed phase, establish UED as a powerful method for mapping out temporally changing molecular structures in chemistry, and potentially, in biology. This review highlights the advances made at Caltech, with emphasis on the principles of UED, its evolution through four generations of instrumentation (UED-1 to UED-4) and its diverse applications.
Co-reporter:Tianbing Xia;Hans-Christian Becker;Chaozhi Wan;Adam Frankel;Richard W. Roberts;
Proceedings of the National Academy of Sciences 2003 100(14) pp:8119-8123
Publication Date(Web):June 18, 2003
DOI:10.1073/pnas.1433099100
The N protein from bacteriophage λ is a key regulator of
transcription antitermination. It specifically recognizes a nascent mRNA stem
loop termed boxB, enabling RNA polymerase to read through downstream
terminators processively. The stacking interaction between Trp-18 of WT N
protein and A7 of boxB RNA is crucial for efficient antitermination.
Here, we report on the direct probing of the dynamics for this interfacial
binding and the correlation of the dynamics with biological functions.
Specifically, we examined the influence of structural changes in four peptides
on the femtosecond dynamics of boxB RNA (2-aminopurine labeled in
different positions), through mutations of critical residues of N peptide
(residues 1–22). We then compare their in vivo (Escherichia
coli) transcription antitermination activities with the dynamics. The
results demonstrate that the RNA–peptide complexes adopt essentially two
dynamical conformations with the time scale for interfacial interaction in the
two structures being vastly different, 1 ps for the stacked structure and
nanosecond for the unstacked one; only the weighted average of the two is
detected in NMR by nuclear Overhauser effect experiments. Strikingly, the
amplitude of the observed ultrafast dynamics depends on the identity of the
amino acid residues that are one helical turn away from Trp-18 in the peptides
and is correlated with the level of biological function of their respective
full-length proteins.
Water molecules at the surface of DNA are critical to its equilibrium
structure, DNA–protein function, and DNA–ligand recognition. Here
we report direct probing of the dynamics of hydration, with femtosecond
resolution, at the surface of a DNA dodecamer duplex whose native structure
remains unperturbed on recognition in minor groove binding with the
bisbenzimide drug (Hoechst 33258). By following the temporal evolution of
fluorescence, we observed two well separated hydration times, 1.4 and 19 ps,
whereas in bulk water the same drug is hydrated with time constants of 0.2 and
1.2 ps. For comparison, we also studied calf thymus DNA for which the
hydration exhibits similar time scales to that of dodecamer DNA. However, the
time-resolved polarization anisotropy is very different for the two types of
DNA and clearly elucidates the rigidity in drug binding and difference in DNA
rotational motions. These results demonstrate that hydration at the surface of
the groove is a dynamical process with two general types of trajectories; the
slowest of them (≈20 ps) are those describing dynamically ordered water.
Because of their ultrafast time scale, the “ordered” water
molecules are the most weakly bound and are accordingly involved in the
entropic (hydration/dehydration) process of recognition.
Water molecules in the DNA grooves are critical for maintaining structural integrity, conformational changes, and molecular
recognition. Here we report studies of site- and sequence-specific hydration dynamics, using 2-aminopurine (Ap) as the intrinsic
fluorescence probe and with femtosecond resolution. The dodecamer d[CGCA(Ap)ATTTGCG]2 was investigated, and we also examined the effect of a specific minor groove-binding drug, pentamidine, on hydration dynamics.
Two time scales were observed: ≈1 ps (bulk-like) and 10–12 ps (weakly bound type), consistent with layer hydration observed
in proteins and DNA. However, for denatured DNA, the cosolvent condition of 40% formamide hydration is very different: it
becomes that of bulk (in the presence of formamide). Well known electron transfer between Ap and nearby bases in stacked assemblies
becomes inefficient in the single-stranded state. The rigidity of Ap in the single strands is significantly higher than that
in bulk water and that attached to deoxyribose, suggesting a unique role for the dynamics of the phosphate-sugar-base in helix
formation. The disparity in minor and major groove hydration is evident because of the site selection of Ap and in the time
scale observed here (in the presence and absence of the drug), which is different by a factor of 2 from that observed in the
minor groove–drug recognition.
Co-reporter:Melanie A. O'Neill;Hans-Christian Becker;Chaozhi Wan;Jacqueline K. Barton
Angewandte Chemie 2003 Volume 115(Issue 47) pp:
Publication Date(Web):8 DEC 2003
DOI:10.1002/ange.200352831
Die ultraschnelle Dynamik des Elektronentransfers (ET) zwischen den Basen der DNA wurde bestimmt, um den Einfluss des „Basenpaar-Gatings“ auf der Zeitskala des Elektronentransports und dessen Temperaturabhängigkeit zu untersuchen. ET tritt lediglich in Doppelhelices auf, die eine spezifische Anordnung der Basen haben (siehe Bild). Die Beschreibung der ET-Dynamik muss unter Berücksichtigung der DNA-Basen-Fluktuation erfolgen.
The dissociation dynamics of trans-azomethane upon excitation to the S1(n,π*) state with a total energy of 93 kcal mol−1is investigated using femtosecond-resolved mass spectrometry in a molecular beam. The transient signal shows an opposite pump–probe excitation feature for the UV (307 nm) and the visible (615 nm) pulses at the perpendicular polarization in comparison with the signal obtained at the parallel polarization: The one-photon symmetry-forbidden process excited by the UV pulse is dominant at the perpendicular polarization, whereas the two-photon symmetry-allowed process initiated by the visible pulse prevails at the parallel polarization. At the perpendicular polarization, we found that the two CN bonds of the molecule break in a stepwise manner, that is, the first CN bond breaks in ≈70 fs followed by the second one in ≈100 fs, with the intermediate characterized. At the parallel polarization, the first CN bond cleavage was found to occur in 100 fs with the intensity of the symmetry-allowed transition being one order of magnitude greater than the intensity of the symmetry-forbidden transition at the perpendicular polarization. Theoretical calculations using time-dependent density functional theory (TDDFT) and the complete active space self-consistent field (CASSCF) method have been carried out to characterize the potential energy surface for the ground state, the low-lying excited states, and the cationic ground state at various levels of theory. Combining the experimental and theoretical results, we identified the elementary steps in the mechanism: The initial driving force of the ultrafast bond-breaking process of trans-azomethane (at the perpendicular polarization) is due to the CNNC torsional motion initiated by the vibronic coupling through an intensity-borrowing mechanism for the symmetry-forbidden n–π* transition. Following this torsional motion and the associated molecular symmetry breaking, an S0/S1conical intersection (CI) can be reached at a torsional angle of 93.1° (predicted at the CASSCF(8,7)/cc-pVDZ level of theory). Funneling through the S0/S1CI could activate the asymmetric CN stretching motion, which is the key motion for the consecutive CN bond breakages on the femtosecond time scale.
Co-reporter:Melanie A. O'Neill;Hans-Christian Becker;Chaozhi Wan;Jacqueline K. Barton
Angewandte Chemie International Edition 2003 Volume 42(Issue 47) pp:
Publication Date(Web):8 DEC 2003
DOI:10.1002/anie.200352831
The ultrafast dynamics of electron transfer (ET) between bases in DNA have been determined to elucidate the critical role of base-pair gating on the timescale of the electron transport and the temperature dependence of the rates. ET occurs only through DNA duplexes that adopt a specific, well-coupled alignment of bases (ET-active; see picture). Descriptions of ET dynamics must include fluctuations of DNA bases.
We report studies of hydration dynamics at the surface of the enzyme protein bovine pancreatic α-chymotrypsin. The probe is
the well known 1-anilinonaphthalene-8-sulfonate, which binds selectively in the native state of the protein, not the molten
globule, as shown by x-ray crystallography. With femtosecond time resolution, we examined the hydration dynamics at two pHs,
when the protein is physiologically in the inactive state (pH 3.6) or the active state (pH 6.7); the global structure and
the binding site remain the same. The hydration correlation function, C(t), whose decay is governed by the rotational and translational motions of water molecules at the site, shows the behavior
observed in this laboratory for other proteins, Subtilisin Carlsberg and Monellin, using the intrinsic amino acid tryptophan as a probe for surface hydration. However, the time scales and amplitudes
vary drastically at the two pHs. For the inactive protein state, C(t) decays with an ultrafast component, close to bulk-type behavior, but 50% of the C(t) decays at a much slower rate, τ = 43 ps. In contrast, for the active state, the ultrafast component becomes dominant (90%)
and the slow component changes to a faster decay, τ = 28 ps. These results indicate that in the active state water molecules
in the hydration layer around the site have a high degree of mobility, whereas in the inactive state the water is more rigidly
structured. For the substrate–enzyme complex, the function and dynamics at the probe site are correlated, and the relevance
to the enzymatic action is clear.
We report studies of hydration dynamics at the surface of the enzyme protein bovine pancreatic α-chymotrypsin. The probe is
the well known 1-anilinonaphthalene-8-sulfonate, which binds selectively in the native state of the protein, not the molten
globule, as shown by x-ray crystallography. With femtosecond time resolution, we examined the hydration dynamics at two pHs,
when the protein is physiologically in the inactive state (pH 3.6) or the active state (pH 6.7); the global structure and
the binding site remain the same. The hydration correlation function, C(t), whose decay is governed by the rotational and translational motions of water molecules at the site, shows the behavior
observed in this laboratory for other proteins, Subtilisin Carlsberg and Monellin, using the intrinsic amino acid tryptophan as a probe for surface hydration. However, the time scales and amplitudes
vary drastically at the two pHs. For the inactive protein state, C(t) decays with an ultrafast component, close to bulk-type behavior, but 50% of the C(t) decays at a much slower rate, τ = 43 ps. In contrast, for the active state, the ultrafast component becomes dominant (90%)
and the slow component changes to a faster decay, τ = 28 ps. These results indicate that in the active state water molecules
in the hydration layer around the site have a high degree of mobility, whereas in the inactive state the water is more rigidly
structured. For the substrate–enzyme complex, the function and dynamics at the probe site are correlated, and the relevance
to the enzymatic action is clear.
We have studied the femtosecond hydration dynamics of Monellin, a protein with a single tryptophan residue at its surface.
Tryptophan was selectively used as a probe of the dynamics, and through monitoring of its fluorescence Stokes shift with time
we obtained the hydration correlation function, which decays due to rotational and translational motions of water at the protein
surface and in bulk. The decay exhibits a “bimodal” behavior with time constants of 1.3 and 16 ps, mirroring relaxation of
the free/quasifree water molecules and surface-bound water layer (minimum binding energy of 1–2 kcal/mol). The observed slow
decay of 16 ps for tryptophan in the native protein differs by more than an order of magnitude from that of bulk water because
of the dynamical exchange in the layer. To examine the effect of unfolding, we also studied hydration dynamics when Monellin
was denatured in a 6 M guanidine hydrochloride solution and obtained a totally different behavior: 3.5 and 56 ps. Comparing
with the results of experiments on free tryptophan in the same concentration of the denaturing solution, we conclude that
the fast component of 3.5 ps comes from bulk-type solvation in the 6 M guanidine hydrochloride. However, the absence of the
16-ps decay and appearance of the 56-ps component reflects a more “rigid solvation,” which is likely to involve the motions
of the protein backbone in the random-coiled state. With the help of polymer theory, this time scale is reproduced in agreement
with experimental observations.
Biological water at the interface of proteins is critical to their equilibrium structures and enzyme function and to phenomena
such as molecular recognition and protein–protein interactions. To actually probe the dynamics of water structure at the surface,
we must examine the protein itself, without disrupting the native structure, and the ultrafast elementary processes of hydration.
Here we report direct study, with femtosecond resolution, of the dynamics of hydration at the surface of the enzyme protein
Subtilisin Carlsberg, whose single Trp residue (Trp-113) was used as an intrinsic biological fluorescent probe. For the protein, we observed two
well separated dynamical solvation times, 0.8 ps and 38 ps, whereas in bulk water, we obtained 180 fs and 1.1 ps. We also
studied a covalently bonded probe at a separation of ≈7 Å and observed the near disappearance of the 38-ps component, with
solvation being practically complete in (time constant) 1.5 ps. The degree of rigidity of the probe (anisotropy decay) and
of the water environment (protein vs. micelle) was also studied. These results show that hydration at the surface is a dynamical
process with two general types of trajectories, those that result from weak interactions with the selected surface site, giving
rise to bulk-type solvation (≈1 ps), and those that have a stronger interaction, enough to define a rigid water structure,
with a solvation time of 38 ps, much slower than that of the bulk. At a distance of ≈7 Å from the surface, essentially all
trajectories are bulk-type. The theoretical framework for these observations is discussed.
Co-reporter:Dongping Zhong;Samir Kumar Pal;Deqiang Zhang;Sunney I. Chan
PNAS 2002 Volume 99 (Issue 1 ) pp:13-18
Publication Date(Web):2002-01-08
DOI:10.1073/pnas.012582399
We report here studies of tryptophan (Trp) solvation dynamics in
water and in the Pyrococcus furiosus rubredoxin protein,
including the native and its apo and denatured forms. We also report
results on energy transfer from Trp to the iron-sulfur [Fe-S]
cluster. Trp fluorescence decay with the onset of solvation dynamics of
the chromophore in water was observed with femtosecond resolution
(≈160 fs; 65% component), but the emission extended to the
picosecond range (1.1 ps; 35% component). In contrast, the decay is
much slower in the native rubredoxin; the Trp fluorescence decay
extends to 10 ps and longer, reflecting the local rigidity imposed by
residues and by the surface water layer. The dynamics of resonance
energy transfer from the two Trps to the [Fe-S] cluster in the
protein was observed to follow a temporal behavior characterized by a
single exponential (15–20 ps) decay. This unusual observation in a
protein indicates that the resonance transfer is to an acceptor of a
well-defined orientation and separation. From studies of the mutant
protein, we show that the two Trp residues have similar energy-transfer
rates. The critical distance for transfer (R0) was
determined, by using the known x-ray data, to be 19.5 Å for Trp-36 and
25.2 Å for Trp-3, respectively. The orientation factor
(κ2) was deduced to be 0.13 for Trp-36, clearly
indicating that molecular orientation of chromophores in the protein
cannot be isotropic with κ2 value of 2/3. These studies
of solvation and energy-transfer dynamics, and of the rotational
anisotropy, of the wild-type protein, the (W3Y, I23V, L32I) mutant, and
the fmetPfRd variant at various pH values reveal a dynamically rigid
protein structure, which is probably related to the
hyperthermophilicity of the protein.
Molecular recognition by biological macromolecules involves many elementary steps, usually convoluted by diffusion processes.
Here we report studies of the dynamics, from the femtosecond to the microsecond time scale, of the different elementary processes
involved in the bimolecular recognition of a protein mimic, cobalt picket-fence porphyrin, with varying oxygen concentration
at controlled temperatures. Electron transfer, bond breakage, and thermal “on” (recombination) and “off” (dissociation) reactions
are the different processes involved. The reaction on-rate is 30 to 60 times smaller than that calculated from standard Smoluchowski
theory. Introducing a two-step recognition model, with reversibility being part of both steps, removes the discrepancy and
provides consistency for the reported thermodynamics, kinetics, and dynamics. The transient intermediates are configurations
defined by the contact between oxygen (diatomic) and the picket-fence porphyrin (macromolecule). This intermediate is critical
in the description of the potential energy landscape but, as shown here, both enthalpic and entropic contributions to the
free energy are important. In the recognition process, the net entropy decrease is −33 cal mol−1 K−1; ΔH is −13.4 kcal mol−1.
Co-reporter:Dongping Zhong;Samir Kumar Pal;Chaozhi Wan
PNAS 2001 Volume 98 (Issue 21 ) pp:11873-11878
Publication Date(Web):2001-10-09
DOI:10.1073/pnas.211440298
In this contribution, we report studies of the primary dynamics of the drug–protein complexes of daunomycin with apo riboflavin-binding
protein. With femtosecond resolution, we observed the ultrafast charge separation between daunomycin and aromatic amino acid
residues of the protein, tryptophan(s). Electron transfer occurs from tryptophan(s) to daunomycin with two reaction times,
1 ps and 6 ps, depending on the local complex structure. The formation of anionic daunomycin radical is crucial for triggering
a series of chemical reactions in redox cycling. One of the subsequent reactions is the reduction of dioxygen to form active
superoxide by the reduced daunomycin. This catalytic process was found to occur within 10 ps. In the absence of dioxygen,
charge recombination takes a much longer time, more than 100 ps. These results, along with similar findings in DNA and nucleotides,
elucidate that the ultrafast generation of reduced daunomycin radicals by photoactivation is a primary step for the observed
photoenhancement of drug cytotoxicity by several orders of magnitude. We also studied the dependence of the dynamics on protein
conformations at different ionic strengths and denaturant concentrations. We observe a sharp transition from the tertiary
structure to the unfolding state at 2 M of denaturant concentration.
Flavoproteins can function as hydrophobic sites for vitamin B2 (riboflavin) or, in other structures, with cofactors for catalytic reactions such as glucose oxidation. In this contribution,
we report direct observation of charge separation and recombination in two flavoproteins: riboflavin-binding protein and glucose
oxidase. With femtosecond resolution, we observed the ultrafast electron transfer from tryptophan(s) to riboflavin in the
riboflavin-binding protein, with two reaction times: ≈100 fs (86% component) and 700 fs (14%). The charge recombination was
observed to take place in 8 ps, as probed by the decay of the charge-separated state and the recovery of the ground state.
The time scale for charge separation and recombination indicates the local structural tightness for the dynamics to occur
that fast and with efficiency of more than 99%. In contrast, in glucose oxidase, electron transfer between flavin-adenine-dinucleotide
and tryptophan(s)/tyrosine(s) takes much longer times, 1.8 ps (75%) and 10 ps (25%); the corresponding charge recombination
occurs on two time scales, 30 ps and nanoseconds, and the efficiency is still more than 97%. The contrast in time scales for
the two structurally different proteins (of the same family) correlates with the distinction in function: hydrophobic recognition
of the vitamin in the former requires a tightly bound structure (ultrafast dynamics), and oxidation-reduction reactions in
the latter prefer the formation of a charge-separated state that lives long enough for chemistry to occur efficiently. Finally,
we also studied the influence on the dynamics of protein conformations at different ionic strengths and denaturant concentrations
and observed the sharp collapse of the hydrophobic cleft and, in contrast, the gradual change of glucose oxidase.
Co-reporter:Chong-Yu Ruan;Ramesh Srinivasan;Boyd M. Goodson;Vladimir A. Lobastov;Hyotcherl Ihee
PNAS 2001 Volume 98 (Issue 13 ) pp:7117-7122
Publication Date(Web):2001-06-19
DOI:10.1073/pnas.131192898
Studies of molecular structures at or near their equilibrium configurations have long provided information on their geometry
in terms of bond distances and angles. Far-from-equilibrium structures are relatively unknown—especially for complex systems—and
generally, neither their dynamics nor their average geometries can be extrapolated from equilibrium values. For such nonequilibrium
structures, vibrational amplitudes and bond distances play a central role in phenomena such as energy redistribution and chemical
reactivity. Ultrafast electron diffraction, which was developed to study transient molecular structures, provides a direct
method for probing the nature of complex molecules far from equilibrium. Here we present our ultrafast electron diffraction
observations of transient structures for two cyclic hydrocarbons. At high internal energies of ≈4 eV, these molecules display
markedly different behavior. For 1,3,5-cycloheptatriene, excitation results in the formation of hot ground-state structures
with bond distances similar to those of the initial structure, but with nearly three times the average vibrational amplitude.
Energy is redistributed within 5 ps, but with a negative temperature characterizing the nonequilibrium population. In contrast,
the ring-opening reaction of 1,3-cyclohexadiene is shown to result in hot structures with a C—C bond distance of over 1.7
Å, which is 0.2 Å away from any expected equilibrium value. Even up to 400 ps, energy remains trapped in large-amplitude motions
comprised of torsion and asymmetric stretching. These studies promise a new direction for studying structural dynamics in
nonequilibrium complex systems.
The anthracycline–DNA complex, which is a potent agent for cancer
chemotherapy, has a unique intercalating molecular structure with
preference to the GC bases of DNA, as shown by Rich's group in studies
of single-crystal x-ray diffraction. Understanding cytotoxicity
and its photoenhancement requires the unraveling of the dynamics under
the solution-phase, physiological condition. Here we report our first
study of the primary processes of drug function. In a series of
experiments involving the drug (daunomycin and adriamycin) in water,
the drug–DNA complexes, the complexes with the four nucleotides (dGTP,
dATP, dCTP, and dTTP), and the drug-apo riboflavin-binding protein, we
show the direct involvement of molecular oxygen and DNA base-drug
charge-separation—the rates for the reduction of the drug and
dioxygen indicate the crucial role of drug/base/O2 in the
efficient and catalytic redox cycling. These dynamical steps, and the
subsequent reactions of the superoxide product(s), can account for the
photoenhanced function of the drug in cells, and potentially for
the cell death.
The cover picture shows the products arising from the dissociation dynamics of cyclobutanone (CB). Unlike simpler linear ketones, CB predissociates anomalously under the Norrish type-I (α-cleavage) reaction mechanism. Investigation of partially deuterated CB isotopomers by femtosecond time-resolved mass spectrometry (shown in the inset), in combination with ab initio calculations, characterized the S0, S1(n,π), and T1(n,π*) potential energy surfaces. The passage through the conical intersection joining the S0 and S1 surfaces follow either gradient difference (x1) or a nonadiabatic coupling (x2) vectors: Following x2, either the hot parent molecule (left) or the acyl diradical (right) is produced; following x1 either the trimethylene and CO (middle) or hot cyclopropane and CO (not shown) are formed. Find out more in the articles by Zewail et al. on pages 273–293 and 294–309.
The dissociation dynamics of two acetone isotopomers ([D0]- and [D6]acetone) after 93 kcal mol−1 (307 nm) excitation to the S1(n,π*) state have been investigated using femtosecond pump–probe mass spectrometry. We found that the nuclear motions of the molecule on the S1 surface involve two time scales. The initial femtosecond motion corresponds to the dephasing of the wave packet out of the Franck–Condon region on the S1 surface. For longer times, the direct observation of the build-up of the acetyl radical confirms that the S1α-cleavage dynamics of acetone is on the nanosecond time scale. Density functional theory and ab initio calculations have been carried out to characterize the potential energy surfaces for the S0, S1, and T1 states of acetone and six other related aliphatic ketones. For acetone, the S1 energy barrier along the single α-positioned carbon–carbon (α-CC) bond-dissociation coordinate (to reach the S0/S1 conical intersection) was calculated to be 18 kcal mol−1 (∼110 kcal mol−1 above the S0 minimum) for the first step of the nonconcerted α-CC bond cleavage; the concerted path is energetically unfavorable, consistent with experiments. The S1 barrier heights for other aliphatic ketones were found to be substantially lower than that of acetone by methyl substitutions at the α-position. The α-CC bond dissociation energy barrier of acetone on the T1 surface was calculated to be only 5 kcal mol−1 (∼90 kcal mol−1 above the S0 minimum), which is substantially lower than the barrier on the S1 surface. Based on the calculations, the α-cleavage reaction mechanism of acetone occurring on the S0, S1, and T1 surfaces can be better understood via a simple physical picture within the framework of valence-bond theory. The theoretical calculations support the conclusion that the observed nanosecond-scale S1 dynamics of acetone below the barrier is governed by a rate-limiting S1T1 intersystem crossing process followed by α-cleavage on the T1 surface. However, at high energies, the α-cleavage can proceed by barrier crossing on the S1 surface, a situation which is demonstrated for cyclobutanone in the accompanying paper.
The anomalous nonradiative dynamics for three cyclobutanone isotopomers ([D0]-, 3,3-[D2]-, and 2,2,4,4-[D4]cyclobutanone) have been investigated using femtosecond (fs) time-resolved mass spectrometry. We have found that the internal motions of the molecules in the S1 state above the dissociation threshold involve two time scales. The fast motion has a time constant of <50 fs, while the slow motion has a time constant of 5.0±1.0, 9.0±1.5, and 6.8±1.0 ps for the [D0], [D2], and [D4] species, respectively. Density functional theory and ab initio calculations have been performed to characterize the potential energy surfaces for the S0, S1(n,π*), and T1(n,π*) states. The dynamic picture for bond breakage is the following: The fast motion represents the rapid dephasing of the initial wave packet out of the Franck–Condon region, whereas the slow motion reflects the α-cleavage dynamics of the Norrish type-I reaction. The redistribution of the internal energy from the initially activated out-of-plane bending modes into the in-plane ring-opening reaction coordinate defines the time scale for intramolecular vibrational energy redistribution (IVR), and the observed picosecond-scale (ps) decay gives the rate of IVR/bond cleavage across the barrier. The observed prominent isotope effect for both [D2] and [D4] isotopomers imply the significance of the ring-puckering and the CO out-of-plane wagging motions to the S1α-cleavage dynamics. The ethylene and ketene (C2 products)—as well as CO and cyclopropane (C3 products)—product ratios can be understood by the involvement of an S0/S1 conical intersection revealed in our calculations. This proposed dynamic picture for the photochemistry of cyclobutanone on the S1 surface can account not only for the abnormally sharp decrease in fluorescence quantum yield and lifetime but also for the dramatic change in the C3:C2 product ratio as a function of increasing excitation energy, as reported by Lee and co-workers (J. C. Hemminger, E. K. C. Lee, J. Chem. Phys.1972, 56, 5284–5295; K. Y. Tang, E. K. C. Lee, J. Phys. Chem.1976, 80, 1833–1836).
Co-reporter:Steven De Feyter, Eric W.-G. Diau and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2000 vol. 2(Issue 4) pp:877-883
Publication Date(Web):07 Feb 2000
DOI:10.1039/A907979C
Using
femtosecond-resolved mass spectrometry in a molecular beam, we report real-time study of the hydrogen
elimination reaction of 1,4-cyclohexadiene. The experimental observation of the ultrafast stepwise H-elimination
elucidates the reaction dynamics and mechanism. With density-functional theory (ground-state)
calculations, the nature of the reaction (multiple) pathways is examined. With the help of recent conical-intersection
calculations, the excited-state and ground-state pathways are correlated. From these experimental
and theoretical results we provide a unifying picture of the
thermochemistry,
photochemistry and
the stereochemistry observed in the condensed phase.
Die Norrish-Typ-II-Spaltung und die McLafferty-Umlagerung, die beide den intramolekularen Transfer eines γ-H-Atoms beinhalten, können auf der Femtosekunden-Zeitskala unterschieden werden. Bei der McLafferty-Umlagerung wird ein Keton in ionische Fragmente gespalten, während bei seiner Norrish-Typ-II-Spaltung ein Diradikal entsteht, das dann entweder cyclisiert oder in Fragmente zerfällt (siehe Schema). Für die Norrish-Typ-II-Spaltung wurde die Dauer des H-Transfers zu 70 – 90 fs bestimmt, und die Lebensdauer des untersuchten Diradikal-Intermediats beträgt 400 – 700 ps.
Das Titelbild zeigt die experimentellen Grundlagen der Femtochemie, des Gebietes, das sich mit der Echtzeitbeobachtung physikalischer, chemischer und biologischer Änderungen auf der Femtosekunden-Zeitskala befasst. Die Zeit wird bei Femtosekunden-Ereignissen mit Hilfe von Laserpulsen bestimmt – mit einem wird die Veränderung ausgelöst, und mit den folgenden werden Schnappschüsse aufgenommen. Die Untersuchung der Bewegung mit atomarer Auflösung verschafft einen Blick auf die molekure Welt wie durchs Fernglas. Mehr über dieses faszinierende Thema findet sich in dem weder gekürzten noch sonstwie adaptierten Nobel-Vortrag von A. H. Zewail auf Seite 2688 ff. – Es ist ganz passend, dass im hinteren Teil dieses Heftes ChemPhysChem erstmals enthalten ist, dessen Erscheinen in früheren Editorials angekündigt wurde.
Über viele Jahrtausende war die Menschheit bestrebt, Vorgänge auf einer immer kürzeren Zeitskala zu verfolgen. In diesem Wettlauf gegen die Zeit ist die Femtosekunden-Zeitauflösung (1 fs=10−15 s) die nicht zu übertrumpfende Errungenschaft im Hinblick auf das Studium der grundlegenden Dynamik der chemischen Bindung. Die Beobachtung genau der Vorgänge, die Chemie zu Wege bringen – die Bildung und der Bruch von Bindungen auf ihren tatsächlichen Zeit- und Längenskalen –, ist der Urquell für das Gebiet der Femtochemie, der Untersuchung molekularer Bewegungen in den bisher nicht beobachtbaren flüchtigen Übergangszuständen physikalischer, chemischer und biologischer Veränderungen. Das Erreichen dieser Auflösung auf atomarer Skala unter Verwendung von ultrakurzen Laserpulsen als Blitzlichtern ist ein Triumph für die Moleküldynamik, ähnlich wie es die Röntgen- und Elektronenbeugung sowie in jüngerer Zeit die Rastertunnelmikroskopie und die NMR-Spektroskopie bei der Untersuchung statischer Molekülstrukturen waren. Auf der Femtosekunden-Zeitskala lassen sich (teilchenartige) Materiewellen erzeugen und ihre kohärente Entwicklung als Einzelmolekül-Trajektorie beobachten. Das Forschungsgebiet nahm seinen Anfang mit der Untersuchung einfacher Systeme aus wenigen Atomen und hat jetzt die Welt des sehr Komplexen in isolierten Systemen, mesoskopischen und kondensierten Phasen und in biologischen Systemen wie Proteinen oder DNA-Strukturen erreicht. Es eröffnet uns außerdem neue Möglichkeiten der Reaktionssteuerung sowie der Struktur-Femtochemie und der Femtobiologie. Die hier vorgelegte Anthologie gibt einen Überblick über die Entwicklung dieses Forschungsgebietes aus einer persönlichen Sicht, umfasst unsere Arbeiten am Caltech und konzentriert sich auf die Entwicklung von Techniken, auf Konzepte und auf neue Entdeckungen.
Norrish type-II and McLafferty rearrangements, which both involve an intramolecular transfer of a γ H atom, can be differentiated on the femtosecond time scale. The McLafferty rearrangement results in ion fragmentation of the parent ketone, whereas the Norrish type-II reaction leads to a diradical species, which then either cyclizes or fragments (see scheme). For Norrish type-II reactions, the reaction time for the transfer of the hydrogen atom is within 70 – 90 fs, and the lifetime of the diradical intermediate is in the range of 400 – 700 ps at the total energy studied.
Co-reporter:Eric W.-G. Diau;Joseph Casanova;John D. Roberts
PNAS 2000 Volume 97 (Issue 4 ) pp:1376-1379
Publication Date(Web):2000-02-15
DOI:10.1073/pnas.030524797
In this communication, we report our femtosecond real-time observation of the dynamics for the three didehydrobenzene molecules
(p-, m-, and o-benzyne) generated from 1,4-, 1,3-, and 1,2-dibromobenzene, respectively, in a molecular beam, by using femtosecond time-resolved
mass spectrometry. The time required for the first and the second C-Br bond breakage is less than 100 fs; the benzyne molecules
are produced within 100 fs and then decay with a lifetime of 400 ps or more. Density functional theory and high-level ab initio calculations are also reported herein to elucidate the energetics along the reaction path. We discuss the dynamics and possible
reaction mechanisms for the disappearance of benzyne intermediates. Our effort focuses on the isolated molecule dynamics of
the three isomers on the femtosecond time scale.
In this contribution, we report studies of the nature of the
dynamics and hydrophobic binding in protein–ligand complexes of human
serum albumin with 2-(2′-hydroxyphenyl)-4-methyloxazole. With
femtosecond time resolution, we examined the orientational motion of
the ligand, its intrinsic nuclear motions, and the lifetime changes in
the hydrophobic phase. For comparisons, with similar but chemical
nanocavities, we also studied the same ligand in micelles and
cyclodextrins. The hydrophobic interactions in the binding crevice are
much stronger than those observed in cyclodextrins and micelles. The
confined geometry restrains the nonradiative decay and significantly
lengthens the excited-state lifetime. The observed dynamics over the
femtosecond-to-nanosecond time scale indicate that the binding
structure is rigid and the local motions of the ligand are nearly
“frozen” in the protein. Another major finding is the elucidation
of the directed dynamics by the protein. Proton transfer and
intramolecular twisting of 2-(2′-hydroxyphenyl)-4-methyloxazole were
observed to evolve along two routes: one involves the direct stretching
motion in the molecular plane (≈200 fs) and is not sensitive to the
environment; the second, less dominant, is related to the twisting
motion (≈3 ps) of the two heterocyclic rings and drastically slows
down in the protein hydrophobic pocket.
Co-reporter:Chaozhi Wan;Torsten Fiebig;Olav Schiemann;Jacqueline K. Barton
PNAS 2000 Volume 97 (Issue 26 ) pp:14052-14055
Publication Date(Web):2000-12-19
DOI:10.1073/pnas.250483297
Charge transfer in supramolecular assemblies of DNA is unique
because of the notion that the π-stacked bases within the duplex may
mediate the transport, possibly leading to damage and/or repair. The
phenomenon of transport through π-stacked arrays over a long distance
has an analogy to conduction in molecular electronics, but the
mechanism still needs to be determined. To decipher the elementary
steps and the mechanism, one has to directly measure the dynamics in
real time and in suitably designed, structurally well characterized DNA
assemblies. Here, we report our first observation of the femtosecond
dynamics of charge transport processes occurring between bases within
duplex DNA. By monitoring the population of an initially excited
2-aminopurine, an isomer of adenine, we can follow the charge transfer
process and measure its rate. We then study the effect of different
bases next to the donor (acceptor), the base sequence, and the distance
dependence between the donor and acceptor. We find that the charge
injection to a nearest neighbor base is crucial and the time scale is
vastly different: 10 ps for guanine and up to 512 ps for inosine.
Depending on the base sequence the transfer can be slowed down or
inhibited, and the distance dependence is dramatic over the range of 14
Å. These observations provide the time scale, and the range and
efficiency of the transfer. The results suggest the invalidity of an
efficient wire-type behavior and indicate that long-range transport is
a slow process of a different mechanism.
The DNA-intercalating chromophore [Ru(phen)2dppz]2+ has unique photophysical properties, the most striking of which is the “light-switch” characteristic when binding to DNA.
As a dimer, it acts as a molecular staple for DNA, exhibiting a remarkable double-intercalating topology. Herein, we report
femtosecond dynamics of the monomeric and the covalently linked dimeric chromophores, both free in aqueous solution and complexed
with DNA. Transient absorption and linear dichroism show the electronic relaxation to the lowest metal-to-ligand charge-transfer
(CT) state, and subpicosecond kinetics have been observed for this chromophore for what is, to our knowledge, the first time.
We observe two distinct relaxation processes in aqueous solution with time constants of 700 fs and 4 ps. Interestingly, these
two time constants are very similar to those observed for the reorientational modes of bulk water. The 700-fs process involves
a major dichroism change. We relate these observations to the change in charge distribution and to the time scales involved
in solvation of the CT state. Slower processes, with lifetimes of ≈7 and 37 ps, were observed for both monomer and dimer when
bound to DNA. Such a difference can be ascribed to the change of the structural and electronic relaxation experienced in the
DNA intercalation pocket. Finally, the recombination lifetime of the final metal-to-ligand CT state to the ground state, which
is a key in the light-switch process, is found in aqueous solution to be sensitive to structural modification, ranging from
260 ps for [Ru(phen)2dppz]2+ and 360 ps for the monomer chromophore derivative to 2.0 ns for the dimer. This large change reflects the direct role of
solvation in the light-switch process.
Co-reporter:Milo M. Lin, Lars Meinhold, Dmitry Shorokhov and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2008 - vol. 10(Issue 29) pp:NaN4239-4239
Publication Date(Web):2008/06/03
DOI:10.1039/B804675C
A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 μs predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.
Co-reporter:Andreas Gahlmann, Sang Tae Park and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2008 - vol. 10(Issue 20) pp:NaN2909-2909
Publication Date(Web):2008/03/31
DOI:10.1039/B802136H
Pulsed electron beams allow for the direct atomic-scale observation of structures with femtosecond to picosecond temporal resolution in a variety of fields ranging from materials science to chemistry and biology, and from the condensed phase to the gas phase. Motivated by recent developments in ultrafast electron diffraction and imaging techniques, we present here a comprehensive account of the fundamental processes involved in electron pulse propagation, and make comparisons with experimental results. The electron pulse, as an ensemble of charged particles, travels under the influence of the space–charge effect and the spread of the momenta among its electrons. The shape and size, as well as the trajectories of the individual electrons, may be altered. The resulting implications on the spatiotemporal resolution capabilities are discussed both for the N-electron pulse and for single-electron coherent packets introduced for microscopy without space–charge.
Physical Chemistry Chemical Physics 2008 - vol. 10(Issue 20) pp:NaN2893-2893
Publication Date(Web):2008/04/01
DOI:10.1039/B801626G
In this perspective we highlight developments and concepts in the field of 4D electron imaging. With spatial and temporal resolutions reaching the picometer and femtosecond, respectively, the field is now embracing ultrafast electron diffraction, crystallography and microscopy. Here, we overview the principles involved in the direct visualization of structural dynamics with applications in chemistry, materials science and biology. The examples include the studies of complex isolated chemical reactions, phase transitions and cellular structures. We conclude with an outlook on the potential of the approach and with some questions that may define new frontiers of research.
Co-reporter:Milo M. Lin, Dmitry Shorokhov and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2009 - vol. 11(Issue 45) pp:NaN10632-10632
Publication Date(Web):2009/09/15
DOI:10.1039/B910794K
Of special interest in molecular biology is the study of structural and conformational changes which are free of the additional effects of the environment. In the present contribution, we report on the ultrafast unfolding dynamics of a large DNA macromolecular ensemble in vacuo for a number of temperature jumps, and make a comparison with the unfolding dynamics of the DNA in aqueous solution. A number of coarse-graining approaches, such as kinetic intermediate structure (KIS) model and ensemble-averaged radial distribution functions, are used to account for the transitional dynamics of the DNA without sacrificing the structural resolution. The studied ensembles of DNA macromolecules were generated using distributed molecular dynamics (MD) simulations, and the ensemble convergence was ensured by monitoring the ensemble-averaged radial distribution functions and KIS unfolding trajectories. Because the order–disorder transition in free DNA implies unzipping, coiling, and strand-separation processes which occur consecutively or competitively depending on the initial and final temperature of the ensemble, DNA order–disorder transition in vacuo cannot be described as a two-state (un)folding process.
Co-reporter:Renske M. van der Veen, Antoine Tissot, Andreas Hauser and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2013 - vol. 15(Issue 20) pp:NaN7838-7838
Publication Date(Web):2013/04/19
DOI:10.1039/C3CP51011E
Four-dimensional (4D) electron microscopy (EM) uniquely combines the high spatial resolution to pinpoint individual nano-objects, with the high temporal resolution necessary to address the dynamics of their laser-induced transformation. Here, using 4D-EM, we demonstrate the in situ irreversible transformation of individual nanoparticles of the molecular framework Fe(pyrazine)Pt(CN)4. The newly formed material exhibits an unusually large negative thermal expansion (i.e. contraction), which is revealed by time-resolved imaging and diffraction. Negative thermal expansion is a unique property exhibited by only few materials. Here we show that the increased flexibility of the metal–cyanide framework after the removal of the bridging pyrazine ligands is responsible for the negative thermal expansion behavior of the new material. This in situ visualization of single nanostructures during reactions should be extendable to other classes of reactive systems.
Co-reporter:María E. Corrales, Vincent Loriot, Garikoitz Balerdi, Jesús González-Vázquez, Rebeca de Nalda, Luis Bañares and Ahmed H. Zewail
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 19) pp:NaN8818-8818
Publication Date(Web):2013/12/24
DOI:10.1039/C3CP54677B
The correlation between chemical structure and dynamics has been explored in a series of molecules with increasing structural complexity in order to investigate its influence on bond cleavage reaction times in a photodissociation event. Femtosecond time-resolved velocity map imaging spectroscopy reveals specificity of the ultrafast carbon–iodine (C–I) bond breakage for a series of linear (unbranched) and branched alkyl iodides, due to the interplay between the pure reaction coordinate and the rest of the degrees of freedom associated with the molecular structure details. Full-dimension time-resolved dynamics calculations support the experimental evidence and provide insight into the structure–dynamics relationship to understand structural control on time-resolved reactivity.
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