Observation of a single protein by ultrafast X-ray diffraction.

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

Time-Resolved Single-Particle X-ray Scattering Reveals Electron-Density Gradients As Coherent Plasmonic-Nanoparticle-Oscillation Source.

Dynamics of optically excited plasmonic nanoparticles are presently understood as a series of scattering events involving the initiation of nanoparticle breathing oscillations. According to established models, these are caused by statistical heat transfer from thermalized electrons to the lattice. An additional contribution by hot-electron pressure accounts for phase mismatches between theory and experimental observations. However, direct experimental studies resolving the breathing-oscillation excitation are still missing. We used optical transient-absorption spectroscopy and time-resolved single-particle X-ray diffractive imaging to access the electron system and lattice. The time-resolved single-particle imaging data provided structural information directly on the onset of the breathing oscillation and confirmed the need for an additional excitation mechanism for thermal expansion. We developed a new model that reproduces all of our experimental observations. We identified optically induced electron density gradients as the initial driving source.

Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging.

One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. Proposed here are two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA), provides a rough classification which is essentially parameter free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs), can generate 3D structures of the objects at any point in the structural landscape. Both these methods are implemented in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and its utility is demonstrated by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern. Both discrete structural classes and continuous deformations are recovered. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility of moving beyond the study of homogeneous sample sets to addressing open questions on topics such as nanocrystal growth and dynamics, as well as phase transitions which have not been externally triggered.

Optimizing the geometry of aerodynamic lens injectors for single-particle coherent diffractive imaging of gold nanoparticles.

Single-particle X-ray diffractive imaging (SPI) of small (bio-)nanoparticles (NPs) requires optimized injectors to collect sufficient diffraction patterns to allow for the reconstruction of the NP structure with high resolution. Typically, aerodynamic lens-stack injectors are used for NP injection. However, current injectors were developed for larger NPs (>100 nm), and their ability to generate high-density NP beams suffers with decreasing NP size. Here, an aerodynamic lens-stack injector with variable geometry and a geometry-optimization procedure are presented. The optimization for 50 nm gold-NP (AuNP) injection using a numerical-simulation infrastructure capable of calculating the carrier-gas flow and the particle trajectories through the injector is also introduced. The simulations were experimentally validated using spherical AuNPs and sucrose NPs. In addition, the optimized injector was compared with the standard-installation 'Uppsala injector' for AuNPs. Results for these heavy particles showed a shift in the particle-beam focus position rather than a change in beam size, which results in a lower gas background for the optimized injector. Optimized aerodynamic lens-stack injectors will allow one to increase NP beam density, reduce the gas background, discover the limits of current injectors and contribute to structure determination of small NPs using SPI.

Controlled beams of shock-frozen, isolated, biological and artificial nanoparticles.

X-ray free-electron lasers promise diffractive imaging of single molecules and nanoparticles with atomic spatial resolution. This relies on the averaging of millions of diffraction patterns of identical particles, which should ideally be isolated in the gas phase and preserved in their native structure. Here, we demonstrated that polystyrene nanospheres and Cydia pomonella granulovirus can be transferred into the gas phase, isolated, and very quickly shock-frozen, i.e., cooled to 4 K within microseconds in a helium-buffer-gas cell, much faster than state-of-the-art approaches. Nanoparticle beams emerging from the cell were characterized using particle-localization microscopy with light-sheet illumination, which allowed for the full reconstruction of the particle beams, focused to < 100 µ m , as well as for the determination of particle flux and number density. The experimental results were quantitatively reproduced and rationalized through particle-trajectory simulations. We propose an optimized setup with cooling rates for particles of few-nanometers on nanosecond timescales. The produced beams of shock-frozen isolated nanoparticles provide a breakthrough in sample delivery, e.g., for diffractive imaging and microscopy or low-temperature nanoscience.

Light-sheet imaging for the recording of transverse absolute density distributions of gas-phase particle-beams from nanoparticle injectors.

Imaging biological molecules in the gas-phase requires novel sample delivery methods, which generally have to be characterized and optimized to produce high-density particle beams. A non-destructive characterization method of the transverse particle beam profile is presented. It enables the characterization of the particle beam in parallel to the collection of, for instance, x-ray-diffraction patterns. As a rather simple experimental method, it requires the generation of a small laser-light sheet using a cylindrical telescope and a microscope. The working principle of this technique was demonstrated for the characterization of the fluid-dynamic-focusing behavior of 220 nm polystyrene beads as prototypical nanoparticles. The particle flux was determined and the velocity distribution was calibrated using Mie-scattering calculations.

Rapid sample delivery for megahertz serial crystallography at X-ray FELs.

Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s-1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.

Vibrational Predissociation of the HCl-(H2O)3 Tetramer.

The vibrational predissociation of the HCl-(H2O)3 tetramer, the largest HCl-(H2O)n cluster for which HCl is not predicted to be ionized, is reported. This work focuses on the predissociation pathway giving rise to H2O + HCl-(H2O)2 following IR laser excitation of the H-bonded OH stretch fundamental. H2O fragments are monitored state selectively by 2 + 1 resonance-enhanced multiphoton ionization (REMPI) combined with time-of-flight mass spectrometry (TOF-MS). Velocity map images of H2O in selected rotational levels are used to determine translational energy distributions from which the internal energy distributions in the pair-correlated cofragments are derived. From the maximum translational energy release, the bond dissociation energy, D0 = 2400 ± 100 cm-1, is determined for the investigated channel. The energy distributions in the fragments are broad, encompassing the entire range of allowed states. The importance of cooperative (nonpairwise) interactions is discussed.

Energetics and Predissociation Dynamics of Small Water, HCl, and Mixed HCl-Water Clusters.

This Review summarizes recent research on vibrational predissociation (VP) of hydrogen-bonded clusters. Specifically, the focus is on breaking of hydrogen bonds following excitation of an intramolecular vibration of the cluster. VP of the water dimer and trimer, HCl clusters, and mixed HCl-water clusters are the major topics, but related work on hydrogen halide dimers and trimers, ammonia clusters, and mixed dimers with polyatomic units are reviewed for completion and comparison. The theoretical focus is on generating accurate potential energy surfaces (PESs) that can be used in detailed dynamical calculations, mainly using the quasiclassical trajectory approach. These PESs have to extend from the region describing large amplitude motion around the minimum to regions where fragments are formed. The experimental methodology exploits velocity map imaging to generate pair-correlated product translational energy distributions from which accurate bond dissociation energies of dimers and trimers and energy disposal in fragments are obtained. The excellent agreement between theory and experiment on bond dissociation energies, energy disposal in fragments, and the contributions of cooperativity demonstrates that it is now possible, with state-of-the-art experimental and theoretical methods, to make accurate predictions about dynamical and energetic properties of dissociating clusters.

Experimental and theoretical investigations of energy transfer and hydrogen-bond breaking in small water and HCl clusters.

Water is one of the most pervasive molecules on earth and other planetary bodies; it is the molecule that is searched for as the presumptive precursor to extraterrestrial life. It is also the paradigm substance illustrating ubiquitous hydrogen bonding (H-bonding) in the gas phase, liquids, crystals, and amorphous solids. Moreover, H-bonding with other molecules and between different molecules is of the utmost importance in chemistry and biology. It is no wonder, then, that for nearly a century theoreticians and experimentalists have tried to understand all aspects of H-bonding and its influence on reactivity. It is somewhat surprising, therefore, that several fundamental aspects of H-bonding that are particularly important for benchmarking theoretical models have remained unexplored experimentally. For example, even the binding strength between two gas-phase water molecules has never been determined with sufficient accuracy for comparison with high-level electronic structure calculations. Likewise, the effect of cooperativity (nonadditivity) in small H-bonded networks is not known with sufficient accuracy. An even greater challenge for both theory and experiment is the description of the dissociation dynamics of H-bonded small clusters upon acquiring vibrational excitation. This is because of the long lifetimes of many clusters, which requires running classical trajectories for many nanoseconds to achieve dissociation. In this Account, we describe recent progress and ongoing research that demonstrates how the combined and complementary efforts of theory and experiment are enlisted to determine bond dissociation energies (D0) of small dimers and cyclic trimers of water and HCl with unprecedented accuracy, describe dissociation dynamics, and assess the effects of cooperativity. The experimental techniques rely on IR excitation of H-bonded X-H stretch vibrations, measuring velocity distributions of fragments in specific rovibrational states, and determining product state distributions at the pair-correlation level. The theoretical methods are based on high-level ab initio potential energy surfaces used in quantum and classical dynamical calculations. We achieve excellent agreement on D0 between theory and experiments for all of the clusters that we have compared, as well as for cooperativity in ring trimers of water and HCl. We also show that both the long-range and the repulsive parts of the potential must be involved in bond breaking. We explain why H-bonds are so resilient and hard to break, and we propose that a common motif in the breaking of cyclic trimers is the opening of the ring following transfer of one quantum of stretch excitation to form open-chain structures that are weakly bound. However, it still takes many vibrational periods to release one monomer fragment from the open-chain structures. Our success with water and HCl dimers and trimers led us to embark on a more ambitious project: studies of mixed water and HCl small clusters. These clusters eventually lead to ionization of HCl and serve as prototypes of acid dissociation in water. Measurements and calculations of such ionizations are yet to be achieved, and we are now characterizing these systems by adding monomers one at a time. We describe our completed work on the HCl-H2O dimer and mention our recent theoretical results on larger mixed clusters.

Experiment and theory elucidate the multichannel predissociation dynamics of the HCl trimer: breaking up is hard to do.

The breaking of hydrogen bonds in molecular systems has profound effects on liquids, e.g., water, biomolecules, e.g., DNA, etc., and so it is no exaggeration to assert the importance of these bonds to living systems. However, despite years of extensive research on hydrogen bonds, many of the details of how these bonds break and the corresponding energy redistribution processes remain poorly understood. Here we report extensive experimental and theoretical insights into the breakup of two or three hydrogen bonds in the dissociation of a paradigm system of a hydrogen-bonded network, the ring HCl trimer. Experimental state-to-state vibrational predissociation dynamics of the trimer following vibrational excitation were studied by using velocity map imaging and resonance-enhanced multiphoton ionization, providing dissociation energies and product state distributions for the trimer's breakup into three separate monomers or into dimer + monomer. Accompanying the experiments are high-level calculations using diffusion Monte Carlo and quasiclassical simulations, whose results validate the experimental ones and further elucidate energy distributions in the products. The calculations make use of a new, highly accurate potential energy surface. Simulations indicate that the dissociation mechanism requires the excitation to first relax into low-frequency motions of the trimer, resulting in the breaking of a single hydrogen bond. This allows the system to explore a critical van der Waals minimum region from which dissociation occurs readily to monomer + dimer.

Experimental and theoretical investigations of the dissociation energy (D0) and dynamics of the water trimer, (H2O)3.

We report a joint experimental-theoretical study of the predissociation dynamics of the water trimer following excitation of the hydrogen bonded OH-stretch fundamental. The bond dissociation energy (D0) for the (H2O)3 → H2O + (H2O)2 dissociation channel is determined from fitting the speed distributions of selected rovibrational states of the water monomer fragment using velocity map imaging. The experimental value, D0 = 2650 ± 150 cm(-1), is in good agreement with the previously determined theoretical value, 2726 ± 30 cm(-1), obtained using an ab initio full-dimensional potential energy surface (PES) together with Diffusion Monte Carlo calculations [ Wang ; Bowman . J. Chem. Phys. 2011 , 135 , 131101 ]. Comparing this value to D0 of the dimer places the contribution of nonpairwise additivity to the hydrogen bonding at 450-500 cm(-1). Quasiclassical trajectory (QCT) calculations using this PES help elucidate the reaction mechanism. The trajectories show that most often one hydrogen bond breaks first, followed by breaking and re-forming of hydrogen bonds (often with different hydrogen bonds breaking) until, after many picoseconds, a water monomer is finally released. The translational energy distributions calculated by QCT for selected rotational levels of the monomer fragment agree with the experimental observations. The product translational and rotational energy distributions calculated by QCT also agree with statistical predictions. The availability of low-lying intermolecular vibrational levels in the dimer fragment is likely to facilitate energy transfer before dissociation occurs, leading to statistical-like product state distributions.

Experimental and theoretical investigations of energy transfer and hydrogen-bond breaking in the water dimer.

The hydrogen bonding in water is dominated by pairwise dimer interactions, and the predissociation of the water dimer following vibrational excitation is reported here. Velocity map imaging was used for an experimental determination of the dissociation energy (D(0)) of (D(2)O)(2). The value obtained, 1244 ± 10 cm(-1) (14.88 ± 0.12 kJ/mol), is in excellent agreement with the calculated value of 1244 ± 5 cm(-1) (14.88 ± 0.06 kJ/mol). This agreement between theory and experiment is as good as the one obtained recently for (H(2)O)(2). In addition, pair-correlated water fragment rovibrational state distributions following vibrational predissociation of (H(2)O)(2) and (D(2)O)(2) were obtained upon excitation of the hydrogen-bonded OH and OD stretch fundamentals, respectively. Quasi-classical trajectory calculations, using an accurate full-dimensional potential energy surface, are in accord with and help to elucidate experiment. Experiment and theory find predominant excitation of the fragment bending mode upon hydrogen bond breaking. A minor channel is also observed in which both fragments are in the ground vibrational state and are highly rotationally excited. The theoretical calculations reveal equal probability of bending excitation in the donor and acceptor subunits, which is a result of interchange of donor and acceptor roles. The rotational distributions associated with the major channel, in which one water fragment has one quantum of bend, and the minor channel with both water fragments in the ground vibrational state are calculated and are in agreement with experiment.

CH···O interaction lowers hydrogen transfer barrier to keto-enol tautomerization of ß-cyclohexanedione: combined infrared spectroscopic and electronic structure calculation study.

Molecular association and keto-enol tautomerization of ß-cyclohexanedione (ß-CHD) have been investigated in argon matrix and also in a thin solid film prepared by depositing pure ß-CHD vapor on a cold (8 K) KBr window. Infrared spectra reveal that, in low-pressure vapor and argon matrix, the molecules are exclusively in diketo tautomeric form. The CH···O hydrogen bonded dimers of the diketo tautomer are produced by annealing the matrix at 28 K. No indication is found for keto-enol tautomerization of ß-CHD in dimeric complexes in argon matrix within the temperature range of 8-28 K. On the other hand, in thin film of pure diketo tautomer, the conversion initiates only when the film is heated at temperatures above 165 K. The observed threshold appears to be associated with excitation of the intermolecular modes, and the IR spectra recorded at high temperatures display narrowing of vibrational bandwidths, which has been associated with reorientations of the molecules in the film. The nonoccurrence of tautomerization of the matrix isolated dimer is consistent with the barrier predicted by electronic structure calculations at B3LYP/6-311++G** and MP2/6-311++G** levels of theory. The transition state calculation predicts that CH···O interaction has a dramatic effect on lowering of the tautomerization barrier, from more than 60 kcal/mol for the bare molecule to ~35-45 kcal/mol for dimers.

Cooperative strengthening of an intramolecular O-H...O hydrogen bond by a weak C-H...O counterpart: matrix-isolation infrared spectroscopy and quantum chemical studies on 3-methyl-1,2-cyclohexanedione.

Matrix-isolation infrared spectra of 1,2-cyclohexanedione (CD) and 3-methyl-1,2-cyclohexanedione (3-MeCD) were measured in a nitrogen matrix at 8 K. The spectral features reveal that, in the matrix environment, both molecules exist exclusively in the monohydroxy tautomeric form, which is stabilized by an intramolecular O-H...O=C hydrogen bond (HB). The nu(O-H) band of the enol tautomer of 3-MeCD appears at a relatively lower frequency and displays a somewhat broader bandwidth compared to that of CD, and these spectral differences between the two molecules are interpreted as being due to the formation of an interconnected C-H...O HB, where the enolic oxygen is the HB acceptor and one of the C-H covalent bonds of the methyl group is the HB donor. Electronic structure calculations at the B3LYP/6-311++G**, MP2/6-311++G**, and MP2/cc-pVTZ levels predict that this tautomer (enol-2) is approximately 3.5 kcal/mol more stable than a second enolic form (enol-1) where such interconnected H-bonding is absent. Theoretical analysis with a series of molecules having similar functional groups reveals that part of the excess stability (approximately 1 kcal/mol) of enol-2 originates from a cooperative interaction between the interconnected C-H...O and O-H...O HBs. In the IR spectrum, a weak band at 3007 cm(-1) is assigned to nu(C-H) of the methyl C-H bond involved in the H-bonded network. The spectra predicted by both harmonic and anharmonic calculations reveal that this transition is largely blue-shifted compared to the fundamentals of the other two methyl C-H stretching frequencies that are not involved in H-bonding. The conclusions are corroborated further by natural bond orbital (NBO) analysis.

Blue shifting C-H...O hydrogen bonded complexes between chloroform and small cyclic ketones: ring-size effects on stability and spectral shifts.

Blue-shifting C-H...O hydrogen bonded complexes between chloroform and three small cyclic ketones (cyclohexanone, cyclopentanone, and cyclobutanone) have been identified by use of FTIR spectroscopy in CCl(4) solution at room temperature. The shifts of the C-H stretching fundamental of chloroform (nu(C-H)) in the said three complexes are +1, +2, and +5 cm(-1), respectively, and the complexation results in enhancement of the nu(C-H) transition intensity in all three cases. The 1:1 stoichiometry of the complexes is suggested by identifying distinct isosbestic points between the carbonyl stretching (nu(C=O)) fundamentals of the monomers and corresponding complexes for spectra measured with different chloroform to ketone concentrations. The nu(C=O) bands in the three complexes are red-shifted by 8, 19, and 6 cm(-1), and apparently have no correlation with the respective blue shifts of the nu(C-H) bands. Spectral analysis reveals that the complex with cyclohexanone is most stable, and the stability decreases with the ring size of the cyclic ketones. A qualitative explanation of the relative stabilities of the complexes is presented by correlating the hydrogen bond acceptor abilities of the carbonyl groups with the ring size of the cyclic ketones. Quantum mechanical calculations at the DFT/B3LYP/6-311++G(d,p) and MP2/6-31+G(d) levels were performed for predictions of the shapes of the complexes, electronic structure parameters of C-H (donor) and C=O (acceptor) groups, intermolecular interaction energies, spectral shifts, and evolution of those properties when the hydrogen bond distance between the donor-acceptor moieties is scanned. The results show that the binding energies of the complexes are correlated with the dipole moments, proton affinity, and n(O) --> sigma*(C-H) hyperconjugative charge transfer abilities of the three ketones. NBO analysis reveals that the blue shifting of the nu(C-H) transition in a complex is the net effect of hyperconjugation and repolarization/rehybridization of the bond under the influence of the electric field of carbonyl oxygen.

Laser induced fluorescence spectroscopy of a mixed dimer between 2-pyridone and 7-azaindole.

We report here the laser induced fluorescence excitation (FE) and dispersed fluorescence (DF) spectra of a 1:1 mixed dimer between 7-azaindole (7AI) and 2-pyridone (2PY) measured in a supersonic free jet expansion of helium. Density functional theoretical calculation at the B3LYP/6-311++G** level has been performed for predictions of the dimer geometry and normal mode vibrational frequencies in the ground electronic state. A planar doubly hydrogen-bonded structure has been predicted to be the most preferred geometry of the dimer. In the FE spectrum, sharp vibronic bands are observed only for excitation of the 2PY moiety. A large number of low-frequency vibronic bands show up in both the FE and DF spectra, and those bands have been assigned to in-plane hydrogen bond vibrations of the dimer. Spectral analyses reveal Duschinsky-type mixing among those modes in the excited state. No distinct vibronic band structure in the FE spectrum was observed corresponding to excitations of the 7AI moiety, and the observation has been explained in terms of nonradiative electronic relaxation routes involving the 2PY moiety.

Hydrogen-bond vibrations in the S(1)<-->S(0) spectra of a nucleobase pair analog: a mixed dimer between 2-pyridone and formamide.

The vibronically resolved electronic spectra for S(1)<-->S(0) transitions of a mixed dimer between 2-pyridone (2PY) and formamide have been measured in a supersonic free jet expansion using laser-induced fluorescence spectroscopy. Quantum chemistry method at different levels of theory has been used to optimize the geometries of the dimer for the S(0) and S(1) electronic states and also to calculate the normal vibrational modes. Assignments for the vibronic bands observed in the dispersed fluorescence spectrum of the 0(0) (0) band have been suggested with the aid of the ground state frequencies calculated by density functional theoretical method. Spectral analysis reveals that electronic excitation causes extensive mixing of the low-frequency intermolecular vibrational modes of the dimer with some of the intramolecular modes of the 2PY moiety. This spectral behavior is consistent with the complete active space self-consistent field theoretical prediction that with respect to a number of geometrical parameters the dimer geometry in S(1) is significantly distorted from the geometry of the S(0) state.