Molecular Movies Research Articles

Making a Molecular Movie with X Rays

Making a Molecular Movie with X Rays

X-rays make molecular movie

X-rays make molecular movie

Following the molecular motion of near-resonant excited CO on Pt(111): A simulated x-ray photoelectron diffraction study based on molecular dynamics calculations

A THz-pump and x-ray-probe experiment is simulated where x-ray photoelectron diffraction (XPD) patterns record the coherent vibrational motion of carbon monoxide molecules adsorbed on a Pt(111) surface. Using molecular dynamics simulations, the excitation of frustrated wagging-type motion of the CO molecules by a few-cycle pulse of 2 THz radiation is calculated. From the atomic coordinates, the time-resolved XPD patterns of the C 1s core level photoelectrons are generated. Due to the direct structural information in these data provided by the forward scattering maximum along the carbon-oxygen direction, the sequence of these patterns represents the equivalent of a molecular movie.

Anatomy of the Photochemical Reaction: Excited-State Dynamics Reveals the C-H Acidity Mechanism of Methoxy Photo-oxidation on Titania.

Light-driven chemical reactions on semiconductor surfaces have potential for addressing energy and pollution needs through efficient chemical synthesis; however, little is known about the time evolution of excited states that determine reaction pathways. Here, we study the photo-oxidation of methoxy (CH3O) derived from methanol on the rutile TiO2(110) surface using ab initio simulations to create a molecular movie of the process. The movie sequence reveals a wealth of information on the reaction intermediates, time scales, and energetics. The reaction is broken in three stages, described by Lewis structures directly derived from the "hole" wave functions that lead to the concept of "photoinduced C-H acidity". The insights gained from this work can be generalized to a set of simple rules that can predict the efficiency of photo-oxidation reactions in reactant-catalyst pairs.

RNA dances to center stage.

RNA dances to center stage.

High-speed AFM imaging.

Proteins are dynamic in nature and function at the single molecule level. To achieve a straightforward and in-depth understanding of their underlying functional mechanism, we need to directly observe protein molecules at work at high resolution, without the use of protein-attached markers. To realize such objectives, high-speed atomic force microscopy (HS-AFM) has been developed and recently its capability has been fully established. This approach opens a new avenue to directly and closely observe individual molecules at submolecular spatial resolution and sub-100 ms time resolution. The captured molecular movies of proteins directly report and provide great insights into how the proteins function. Moreover, the very recent progress of HS-AFM technology has extended its use to the observation of dynamic cellular processes. In this article, I review imaging studies to show the innovative power and potential of this new microscopy.

Tracking chemical reactions with ultrafast X-ray spectroscopies and scattering

Ultrafast structural dynamics is an emerging field aiming to deliver a detailed understanding of the elementary steps in reacting chemical species, which involve changes in their nuclear, electronic and spin states. Such processes are vital ingredients in chemistry and biology, but also in technological applications, including efficient charge transport in solar energy converters and ultrafast switchable molecular magnets. In order to unravel the complex dynamic behavior in photoexcited molecules we have implemented a suite of ultrafast x-ray spectroscopic and scattering tools to zoom into both the electronic and nuclear structures, with the goal to ultimately deliver a molecular movie of ongoing chemical processes. In view of the many potential applications in chemical and biological dynamics it is desirable to increase the signal-to-noise (S/N) level of such experiments as well as to decrease the time resolution into the femtosecond time domain. We present our benchmark results using a versatile setup that permits simultaneous measurements of ultrafast x-ray absorption and emission spectroscopies combined with x-ray diffuse scattering. This combined scattering and spectroscopic approach has recently been established by us at different synchrotron [1-2] and XFEL [3] lightsources. We applied it to study different photochemical systems in liquid media, ranging from nascent radicals in solution to photocatalytic systems, with the goal to deliver a deeper understanding of the elementary steps in chemical reactivity.

Molecular movies: Ultrafast measurements on structural dynamics of crystals and technology developments in ultrafast science

Molecular movies : ultrafast measurements on structural dynamics of crystals and technology developments in ultrafast science Ultrafast science is an exciting physics field, enabling us to observe atoms moving within matter upon photo-excitation. Using electron 'probe' pulses and laser 'pump' pulses, we monitor dynamics in remarkable short time scales (10-15/s) with microscopic precision (10-11/m). We investigate an ultrafast insulator-to-metal transition in TSe2 and TaSe2 crystals.

Tabletop imaging of structural evolutions in chemical reactions demonstrated for the acetylene cation.

The introduction of femto-chemistry has made it a primary goal to follow the nuclear and electronic evolution of a molecule in time and space as it undergoes a chemical reaction. Using Coulomb Explosion Imaging, we have shot the first high-resolution molecular movie of a to and fro isomerization process in the acetylene cation. So far, this kind of phenomenon could only be observed using vacuum ultraviolet light from a free-electron laser. Here we show that 266 nm ultrashort laser pulses are capable of initiating rich dynamics through multiphoton ionization. With our generally applicable tabletop approach that can be used for other small organic molecules, we have investigated two basic chemical reactions simultaneously: proton migration and C=C bond breaking, triggered by multiphoton ionization. The experimental results are in excellent agreement with the timescales and relaxation pathways predicted by new and quantitative ab initio trajectory simulations.

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

The dioxygen we breathe is formed from water by its light-induced oxidation in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction center is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2 flash (2F) and 3 flash (3F) photosystem II samples, and of a transient 3F′ state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn-reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.

Catalytic strategy used by the myosin motor to hydrolyze ATP.

Myosin is a molecular motor responsible for biological motions such as muscle contraction and intracellular cargo transport, for which it hydrolyzes adenosine 5'-triphosphate (ATP). Early steps of the mechanism by which myosin catalyzes ATP hydrolysis have been investigated, but still missing are the structure of the final ADP·inorganic phosphate (Pi) product and the complete pathway leading to it. Here, a comprehensive description of the catalytic strategy of myosin is formulated, based on combined quantum-classical molecular mechanics calculations. A full exploration of catalytic pathways was performed and a final product structure was found that is consistent with all experiments. Molecular movies of the relevant pathways show the different reorganizations of the H-bond network that lead to the final product, whose γ-phosphate is not in the previously reported HPγO4(2-) state, but in the H2PγO4(-) state. The simulations reveal that the catalytic strategy of myosin employs a three-pronged tactic: (i) Stabilization of the γ-phosphate of ATP in a dissociated metaphosphate (PγO3(-)) state. (ii) Polarization of the attacking water molecule, to abstract a proton from that water. (iii) Formation of multiple proton wires in the active site, for efficient transfer of the abstracted proton to various product precursors. The specific role played in this strategy by each of the three loops enclosing ATP is identified unambiguously. It explains how the precise timing of the ATPase activation during the force generating cycle is achieved in myosin. The catalytic strategy described here for myosin is likely to be very similar in most nucleotide hydrolyzing enzymes.

Progress toward time-resolved molecular imaging: A theoretical study of optimal parameters in static photoelectron holography

The availability of short-pulse free-electron lasers has led to the idea of using photoelectron holography as a method of directly imaging molecular dissociations or reactions in real time, as, e.g., in a recent theoretical study by Krasniqi et al., [F. Krasniqi, B. Najjari, L. Str\"uder, D. Rolles, A. Voitkiv, and J. Ullrich, Phys. Rev. A 81, 033411 (2010)]. In this paper, we extend this earlier work and in particular look at two critical questions concerning the optimum type of data required for such holographic imaging: the choice of photoelectron kinetic energy (e.g., $\ensuremath{\sim}$300 eV versus $\ensuremath{\sim}$1700 eV as in the prior study), and the use of a single energy or multiple energies. After verifying that our calculations fully duplicate those in this prior paper, we show that using lower energies is preferable to using higher energies for image quality, a conclusion consistent with prior photoelectron holography studies at surfaces, and that multiple lower energies in which the hologram effectively spans a volume in $k$space yields the best quality images that should be useful for such ``molecular movies.'' Although the amount of data required for such multi-energy holography is roughly an order of magnitude higher than that for single energy, the reduction of artifacts and the improved quality of the images suggest this as the optimum ultimate future strategy for such dynamic imaging.

Towards simultaneous measurements of electronic and structural properties in ultra-fast x-ray free electron laser absorption spectroscopy experiments

The rapidly growing ultrafast science with X-ray lasers unveils atomic scale processes with unprecedented time resolution bringing the so called “molecular movie” within reach. X-ray absorption spectroscopy is one of the most powerful x-ray techniques providing both local atomic order and electronic structure when coupled with ad-hoc theory. Collecting absorption spectra within few x-ray pulses is possible only in a dispersive setup. We demonstrate ultrafast time-resolved measurements of the LIII-edge x-ray absorption near-edge spectra of irreversibly laser excited Molybdenum using an average of only few x-ray pulses with a signal to noise ratio limited only by the saturation level of the detector. The simplicity of the experimental set-up makes this technique versatile and applicable for a wide range of pump-probe experiments, particularly in the case of non-reversible processes.

High-Order Harmonic Generation Driven by Two-Color Laser Fields

In the past three decades, high-order harmonic generation (HHG) has attracted much attention due to its promising applications on creating table-top coherent extreme-ultraviolet (EUV/XUV) or X-ray sources, synthesizing attosecond pulses, probing electron dynamics and making ”molecular movies”, etc. We review our recent experimental and theoretical progresses in HHG driven by two-color laser fields, including broadening of XUV supercontinuum, generation of isolated attosecond pulses (IAPs), selection of long or short quantum trajectories, enhancement of HHG yield, creation of wavelength-tunable, bandwidth-controlled XUV emission, etc.

Xfels for Imaging Molecular Dynamics

The recent invention of the hard X-ray laser has created a host of new opportunities for the study of atomic processes and dynamics in many fields. Since the Linac Coherent Light Source (LCLS) started operation in late 2009 at SLAC we have collected femtosecond pulsed coherent X-ray scattering from many molecular systems. It has been found that sufficiently brief X-ray pulses terminate before radiation damage commences, opening up many opportunities for new experiments in time- resolved imaging with atomic spatial resolution at room temperature, in condensed matter physics, materials science and biology. I will review some of this work, undertaken in collaboration with many others, including pump-probe experiments on the large molecular complexes involved in photosynthesis, and on a drug target molecule for sleeping sickness. A new approach to disentangling orientational disorder will also be demonstrated, aimed at reconstructing the image of one molecule, using the scattering from many in random orientations in solution, without modeling, based on angular correlation functions. A new single-particle injection scheme will be described to synchronize X-ray pulse emission with particle injection. Prospects for the formation of “molecular movies” which track chemical reactions will be outlined. I'll also describe the new approaches to the phase problem which these experiments suggest. A review of all this work can be found in Rev Mod Phys. 75, 102601 (2012)

Organic’s Past Is Prologue

It can be tough to leave a memorable impression when you are the last conference speaker of a long day, three days into a scientific conference. The University of Tokyo’s Eiichi Nakamura, however, wasn’t fazed. “I promise you this won’t be boring,” Nakamura assured an auditorium’s worth of chemists at the 2013 National Organic Chemistry Symposium (NOS). “I’m going to show you molecular movies.” As the conference-goers settled in, some surreptitiously sipped wine they secreted in from the evening’s banquet, past the watchful eyes of ushers instructed to keep food and drink out of the hall. Not long after the lights dimmed, Nakamura clicked “play” on black-and-white footage of real molecules twisting and turning inside carbon nanotubes, visible to human eyes in a way unimaginable a generation ago. Nakamura and his collaborators began making microscopic motion pictures in 2007, and they continue to explore new questions with the technology. Nakamura ...

Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 \AA{} and ${10}^{\ensuremath{\circ}}$, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a $4\ensuremath{\pi}$ detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a ``molecular movie.''

Strongly aligned and oriented molecular samples at a kHz repetition rate

We demonstrate strong adiabatic laser alignment and mixed-field orientation at kHz repetition rates. We observe the degrees of alignment as large as ⟨cos2θ⟩2D=0.94 at 1 kHz operation for iodobenzene. The experimental setup consists of a kHz laser system simultaneously producing pulses of 30 fs (1.3 mJ) and 450 ps (9 mJ). A cold 1-K state-selected molecular beam is produced at the same rate by appropriate operation of an Even–Lavie valve. Quantum state selection has been obtained using an electrostatic deflector. A camera and data acquisition system records and analyses the images on a single-shot basis. The system is capable of producing, controlling (translation and rotation) and analysing cold molecular beams at kHz repetition rates and is therefore ideally suited for the recording of ultrafast dynamics in so-called ‘molecular movies’.

High-speed atomic force microscopy

High-speed atomic force microscopy (HS-AFM) has been developed as a nano-dynamics visualization technique. This microscopy permits direct observation of structure dynamics and dynamic processes of biological molecules in physiological solutions, at a subsecond to sub-100 ms temporal resolution and an ∼2 nm lateral and a 0.1 nm vertical resolution. Importantly, tip-sample interactions do not disturb the biomolecules' functions. Various functioning proteins including myosin V walking on an actin filament and bacteriorhodopsin responding to light have been successfully visualized with HS-AFM. In the quest for understanding the functional mechanisms of proteins, inferences no longer have to be made from static snapshots of molecular structures and dynamic behavior of optical markers attached to proteins. High-resolution molecular movies obtained from HS-AFM observations reveal the details of molecules' dynamic behavior in action, without the need for intricate analyses and interpretations. In this review, I first describe the fundamentals behind the achieved high imaging rate and low invasiveness to samples, and then highlight recent imaging studies. Finally, future studies are briefly described.

Filming Dynamic Processes of Proteins by High-Speed Afm

Directly observing individual protein molecules in action at high spatiotemporal resolution has long been the holy grail for biological science. High-speed atomic force microscopy (HS-AFM) which can perform this type of observations is now materialized. It opens up a new opportunity to directly observe the structure dynamics and dynamic processes of biological molecules in physiological solutions, at subsecond to sub-100 ms temporal resolution and ∼2 nm lateral and 0.1 nm vertical spatial resolution. Importantly, the tip-sample interaction does not disturb their function. In fact, functioning molecules, such as myosin V walking on an actin filament and bacteriorhodopsin in response to light, have been successfully visualized. In the quest for the functional mechanism of proteins, inferences no longer have to be made from static snapshots of their molecular structures and dynamic behavior of optical markers attached to proteins. High-resolution molecular movies reveal the details of dynamic behavior of molecules in action, which can be interpreted without intricate analyses and interpretations. In this talk, I will highlight recent imaging studies and then describe the fundamentals behind the achieved high imaging rate and low-invasiveness to the sample.