Ab initio studies of ultrafast x-ray scattering of the photodissociation of iodine

We computationally examine various aspects of the reaction dynamics of the photodissociation and recombination of molecular iodine. We use our recently proposed formalism to calculate time-dependent x-ray scattering signal changes from first principles. Different aspects of the dynamics of this prototypical reaction are studied, such as coherent and noncoherent processes, features of structural relaxation that are periodic in time versus nonperiodic dissociative processes, as well as small electron density changes caused by electronic excitation, all with respect to x-ray scattering. We can demonstrate that wide-angle x-ray scattering offers a possibility to study the changes in electron densities in nonperiodic systems, which render it a suitable technique for the investigation of chemical reactions from a structural dynamics point of view.     

Advantages of time-resolved difference X-ray solution scattering curves in analyzing solute molecular structure

Time-resolved X-ray solution scattering provides a powerful method for investigating reaction dynamics in the solution phase. Since X-rays scatter from all atoms in the solution sample, the scattering intensity is contributed from not only the solute but also the solvent and the solute–solvent cross terms. For a typical concentration the solvent molecules outnumber the solute molecules and thus the relative sensitivity of the scattering intensity to the solute structure is extremely low. To increase the structural sensitivity to the solute and to extract only the signal from structural changes, time-resolved difference scattering signal is obtained by subtracting the original raw scattering curve at a negative reference time delay from that at a positive time delay. Here we show and emphasize that time-resolved difference X-ray scattering curves generally exhibit higher structural sensitivity to the solute molecular structure and lower influence from experimental background and imperfection of theory than original raw scattering curves. These characteristics justify the validity of fitting models to difference curves to obtain transient structural information even when the magnitude of the time-resolved difference curves is smaller than the discrepancy between the theory and experiment for the original scattering curve. We considered small molecules and proteins in solution probed by time-resolved X-ray solution scattering.     

Measurement of the field-free alignment of diatomic molecules

An apparatus was constructed to experimentally quantify the field-free alignment of diatomic molecules irradiated by strong femtosecond laser pulses. In this apparatus, both homodyne and pure heterodyne detections were realized. The alignment signal is proportional to [ - 1/3](2) for homodyne detection and ( - 1/3) for pure heterodyne detection, where theta is the polar angle between the molecular axis and the laser polarization direction. Fourier transform spectra of the homodyne signal and the pure heterodyne signal were also studied. By comparing the alignment signal and its Fourier transform spectrum with the numerical calculation of the time-dependent Schr?dinger equation, we demonstrated that the pure heterodyne signal directly reproduced the alignment parameter , and its Fourier transform spectrum provided information regarding the populations of different J states in the rotational wavepacket.     

Stretched poly(dimethylsiloxane) gels as NMR alignment media for apolar and weakly polar organic solvents: an ideal tool for measuring RDCs at low molecular concentrations

The measurement of residual dipolar couplings (RDCs), meanwhile a standard method for obtaining structural information in biomolecular NMR, requires partial alignment of the sample. Special demands on alignment media so far limit the applicability of this approach to small molecules in organic solvents. Major limitations are the free scalability of alignment and the suppression of residual signals of the alignment medium to allow effective measurement of low-concentration samples. Here, we present stretched poly(dimethylsiloxane) (PDMS) cross-linked by beta-rays as an alignment medium with no visible impurities in 1H NMR spectra but a single signal at approximately 0.1 ppm that can easily be removed by slightly modified water suppression methods. Besides the free scalability, its applicability to the measurement of RDCs in small molecules at low concentration is demonstrated on a approximately 12 mM sample of spiroindene. The induced alignment tensor in this case can be predicted reasonably well by a simplified model on the basis of steric interactions only.     

Nanosecond photofragment imaging of adiabatic molecular alignment

Adiabatic alignment of CH(3)I, induced by the anisotropic interaction of this symmetric top molecule with the intense field of a nonresonant infrared laser pulse, has been studied using velocity map imaging. We are using photodissociation imaging with pulsed nanosecond lasers to probe the distribution of the molecular axis in the laboratory space. In contrast to the commonly used probing with femtosecond laser pulses, this technique directly yields the degree of alignment over an extended space-time volume. This will be relevant for future reactive scattering experiments with laser-aligned molecules. The obtained degree of alignment, (cos?(2)θ), measured as a function of the infrared laser intensity, agrees well with a quantum calculation for rotationally cold methyl iodide. The strong infrared laser is also found to modify the photofragmentation dynamics and open up pathways to CH(3)I(+) formation and subsequent fragmentation.     

Alignment of ethyl halide molecules (C2H5X, X= I, Br, Cl) induced by strong ps laser irradiation

The alignment of polyatomic molecules under strong 35 ps laser irradiation is investigated for a broad range of laser intensities (10(13)-10(15) W/cm(2)) using time-of-flight mass spectrometry. The dynamic alignment of the molecules under study (C2H5X, X = I, Br, Cl) is verified in single-pulse experiments by recording the fragments' angular distributions, their dependence on the laser intensity, and also the comparison of the ionic signal of the various fragments recorded for linear and circular polarization. For all cases, the angular distributions of the Coulomb explosion fragments are found to be independent of the laser peak intensity, implying that the molecular alignment is taking place during the rise time of the laser pulses at relatively low intensities (approximately 10(13) W/cm(2)). Moreover, the same result implies that the alignment mechanism is close to the adiabatic limit, albeit the laser pulse duration is much shorter than the characteristic rotational times (1/2B) of the molecules under study. Finally, by comparing the angular distributions of the different molecules, we conclude that the degree of alignment is only weakly dependent on the molecular mass and the moment of inertia under the irradiation conditions applied.     

Anisotropic Picosecond X-ray Solution Scattering from Photo-selectively Aligned Protein Molecules

Anisotropic X-ray scattering patterns of transiently aligned protein molecules in solution are measured by using pump-probe X-ray solution scattering. When a linearly polarized laser pulse interacts with an ensemble of molecules, the population of excited molecules is created with their transition dipoles preferentially aligned along the laser polarization direction. We measured the X-ray scattering from the myoglobin protein molecules excited by a linearly polarized, short laser pulse and obtained anisotropic scattering patterns on 100 ps time scale. An anisotropic scattering pattern contains higher structural information content than a typical isotropic pattern available from randomly oriented molecules. In addition, multiple independent diffraction patterns measured by using various laser polarization orientations will give substantially increased amount of structural information compared with a single isotropic pattern. By monitoring the temporal change of the anisotropic scattering pattern from 100 ps to 1 μs, we observed the orientational dynamics of photo-generated myoglobin with the rotational diffusion time of ～15 ns.     

Watching Orientational Ordering at the Nanoscale with Coherent Anti‐Stokes Raman Microscopy

Whether in lipid membranes, liquid crystals or solid‐state catalysts, the orientational ordering of molecules greatly influences the overall system behaviour. However, watching molecular alignment is a huge technical challenge. This article introduces nonlinear Raman (coherent anti‐Stokes Raman scattering; CARS) microscopy as a promising tool for fast, label‐free 3D chemical and structural sample characterization at the nanoscale in real time.     

High-resolution small-angle x-ray investigations on poly-o-bromostyrene in benzene solutions

Small-angle x-ray investigations on poly-o-bromostyrene in benzene solution at extremely high resolution (corresponding to a Bragg's value of 3200 Å) proved to be able to link together the ranges covered by small-angle x-ray scattering and light scattering. On the other hand, there are problems encountered in molecular weight determination of chain molecules, since both methods at extremely small angles and at finite concentrations reach the limits of particle scattering. The differing results obtained by means of the two methods for the molecular weight of a rather high molecular weight sample of poly-o-bromostyrene are ascribed to entangelements stabilized by dipole–dipole interactions. These, due to the differing Bragg's angles and concentration ranges in the two methods, affect the experimental results to a different degree.     

Field-induced alignment of a smectic-A phase: a time-resolved x-ray diffraction investigation

The field-induced alignment of a smectic-A phase is, in principle, a complicated process involving the director rotation via the interaction with the field and the layer rotation via the molecular interactions. Time-resolved nuclear magnetic resonance spectroscopy has revealed this complexity in the case of the director alignment, but provides no direct information on the motion of the layers. Here we describe a time-resolved x-ray diffraction experiment using synchrotron radiation to solve the challenging problem of capturing the diffraction pattern on a time scale which is fast in comparison with that for the alignment of the smectic layers. We have investigated the alignment of the smectic-A phase of 4-octyl-4(')-cyanobiphenyl by a magnetic field. The experiment consists of creating a monodomain sample of the smectic-A phase by slow cooling from the nematic phase in a magnetic field with a flux density of 7 T. The sample is then turned quickly through an angle phi(0) about an axis parallel to the x-ray beam direction but orthogonal to the field. A sequence of two-dimensional small angle x-ray diffraction patterns are then collected at short time intervals. Experiments were carried out for different values of phi(0), and at different temperatures. The results show that the alignment behavior changes fundamentally when phi(0) exceeds 45 degrees, and that there is a sharp change in the alignment process when the temperature is less than 3 degrees C below the smectic-A-nematic transition. The results of the x-ray experiments are in broad agreement with the NMR results, but reveal major phenomena concerning the maintenance of the integrity of the smectic-A layer structure during the alignment process.     

Alignment of molecules by the Monte Carlo optimization of molecular similarity indices

3D-QSAR uses statistical techniques to correlate calculated structural properties with target properties like biological activity. The comparison of calculated structural properties is dependent upon the relative orientations of molecules in a given data set. Typically molecules are aligned by performing an overlap of common structural units. This “alignment rule” is adequate for a data set, that is closely related structurally, but is far more difficult to apply to either a diverse data set or on the basis of some structural property other than shape, even for sterically similar molecules. In this work we describe a new algorithm for molecular alignment based upon optimization of molecular similarity indices. We show that this Monte Carlo based algorithm is more effective and robust than other optimizers applied previously to the similarity based alignment problem. We show that QSARs derived using the alignments generated by our algorithm are superior to QSARs derived using the more common alignment of fitting of common structural units. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1344–1353, 1997     

Nonadiabatic alignment of asymmetric top molecules: rotational revivals

The rotational revival structure of asymmetric top molecules, following irradiation by an intense picosecond laser pulse, is explored theoretically and experimentally. Numerically we solve nonperturbatively for the rotational dynamics of a general asymmetric top subject to a linearly polarized intense pulse, and analyze the dependence of the dynamical alignment on the field and system parameters. Experimentally we use time-resolved photofragment imaging to measure the alignment of two molecules with different asymmetry, iodobenzene, and iodopentafluorobenzene. Our numerical results explain the experimental observations and generalize them to other molecules. The rotational revival structure of asymmetric tops differs qualitatively from the intensively studied linear top case. Potentially it provides valuable structural information about molecules.     

On the possibility of aligning paramagnetic molecules or ions in a magnetic field

Strong magnetic fields can hybridize low rotational states of paramagnetic molecules or molecular ions whose electronic angular momentum is coupled to the molecular axis. The hybridization creates pendular states in which the molecular axis is confined to librate over a limited angular range about the field direction. In this way substantial spatial alignment associated with large Zeeman shifts can be attained for many ground-state radicals or ions and electronically excited states of diatomic or linear molecules. The magnetic hybridization is analogous to that recently demonstrated for polar molecules in electric fields. The magnetic version can only provide ensemble alignment rather than orientation, but offers complementary chemical scope by virtue of its applicability to nonpolar molecules and ions.     

Post-source decay of alkylated and functionalized polycyclic aromatic compounds

Post-source decay (PSD) is a valuable tool for providing structural information from large molecules by time-of-flight mass spectrometry (TOFMS). We used PSD to obtain this type of data from small molecules in the laser desorption/ionization (LDI) study of diesel engine exhaust particles. As the original nitrogen laser (lambda = 337 nm, E = 3.5 eV/photon) of our TOF mass spectrometer does not yield sufficient energy to ionize polycyclic aromatic hydrocarbons (PAHs), a second laser with a shorter wavelength has been coupled to the instrument. The fourth harmonic of a Nd:YAG laser (lambda = 266 nm, 4.6 eV/photon) has been chosen to achieve two-photon single-step desorption/ionization of PAHs. The PSD fragmentation of functionalized, alkylated and sulfur PAHs is discussed. Diesel engine exhaust particles are also studied as an example of a real complex sample. This technique is presented herein as a way to identify small molecules in environmental samples. Information provided by LDI-PSD-TOFMS can be a way to distinguish pollutants with very close molecular weights even if the resolving power of a TOF mass spectrometer is not sufficient.     

Analysis and simulation of the structure of nanoparticles that undergo a surface-driven structural transformation

A room temperature solid-state structural transformation was observed in 3 nm ZnS nanoparticles in methanol following the addition of water (Zhang et al., Nature 424, 1025, 2003). Experimental wide angle x-ray scattering (WAXS), x-ray absorption near edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) spectroscopy measurements show a large increase in crystallinity associated with water addition, in agreement with molecular dynamics (MD) predictions. Here we perform first-shell EXAFS and pair distribution function analysis and whole-nanoparticle calculations of WAXS, EXAFS and XANES to compare structural data with the MD predictions. The predicted WAXS patterns give excellent agreement with data, while the predicted EXAFS and XANES spectra give poor agreement. Relative to WAXS, XANES and EXAFS spectra contain additional structural information related to the distribution of disorder. The discrepancy between the x-ray diffraction and x-ray absorption results indicates that structural disorder is partitioned between interior and surface regions more strongly than predicted in the MD simulations.     

In situ dynamic measurements of the enhanced SERS signal using an optoelectrofluidic SERS platform

A novel active surface-enhanced Raman scattering (SERS) platform for dynamic on-demand generation of SERS active sites based on optoelectrofluidics is presented in this paper. When a laser source is projected into a sample solution containing metal nanoparticles in an optoelectrofluidic device and an alternating current (ac) electric field is applied, the metal nanoparticles are spontaneously concentrated and assembled within the laser spot, form SERS-active sites, and enhance the Raman signal significantly, allowing dynamic and more sensitive SERS detection. In this simple platform, in which a glass slide-like optoelectrofluidic device is integrated into a conventional SERS detection system, both dynamic concentration of metal nanoparticles and in situ detection of SERS signal are simultaneously possible with only a single laser source. This optoelectrofluidic SERS spectroscopy allows on-demand generation of 'hot spots' at specific regions of interest, and highly sensitive, reliable, and stable SERS measurements of the target molecules in a tiny volume (～500 nL) of liquid sample without any fluidic components and complicated systems.     

Determination of Complex Small‐Molecule Structures Using Molecular Alignment Simulation

Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy‐based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule‐specific anisotropic NMR parameters. The quantitative correlation uses an accurate three‐dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ‐benzyl‐l ‐glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.     

Comparative studies of structural properties and conformational changes of proteins by analytical ultracentrifugation and other techniques

Analytical ultracentrifugation is a powerful tool for investigating the size of proteins in solution, especially by measuring sedimentation and diffusion coefficients and molar masses. Several further molecular parameters such as frictional ratios, axial ratios of hydrodynamic models, and Stokes radii allow a rough estimate of the protein overall structure. Sedimentation analysis may also be applied efficaciously for monitoring conformational changes of proteins occurring upon ligand binding or denaturation. For the determination of very small changes in shape, however, great care and a series of precautions are required. We investigated the enzymes citrate synthase and malate synthase in the absence and in the presence of ligands, in order to study the structural properties of the proteins and their ligand complexes. We also compared the results of the ultracentrifugal analysis with the results of other solution techniques such as UV absorption, fluorescence spectroscopy, circular dichroism, and small-angle x-ray scattering on the one hand, and the crystallographic 3D structure of citrate synthase on the other. The spectroscopic methods may be used as efficient and rapid tools for screening the occurrence of conformational changes caused by alterations of chromophores and fluorophores. The structural information provided by small-angle scattering (e.g., radii of gyration, maximum particle diameters, vclumes and surface areas) can be used to establish quantitative correlations between solution scattering and hydrodynamic data. In this context, however, knowledge or qualified assumptions of partial specific volumes and hydration are additionally required. Good agreement was reached between small-angle scattering and ultracentrifugal data, and also with crystallographic data if protein hydration was considered properly. The given approaches may be used to predict hydrodynamic properties if x-ray data are available, and for many verifications of other structural data, e.g., Stokes radii, diffusion coefficients, axial and frictional ratios determined by independent methods.Abbreviations materials AcCoA acetyl coenzyme A - CoA coenzyme A - CS citrate synthase (EC 4.1.3.7) - DTT dithiothreitol - GdrnCl guanidinium chloride - MS malate synthase (EC 4.1.3.2.)Methods - AUC analytical ultracentrifugation - CD circular dichroism - EM fluorescence emission spectroscopy - EX fluorescence excitation spectroscopy - SAS small-angle scattering - SAXS small-angle x-ray scattering - UV ultraviolet absorption spectroscopy - XD x-ray diffraction Models OE oblate ellipsoidal model - PE prolate ellipsoidal model     

Spatiotemporal Kinetics in Solution Studied by Time‐Resolved X‐Ray Liquidography (Solution Scattering)

Information about temporally varying molecular structure during chemical processes is crucial for understanding the mechanism and function of a chemical reaction. Using ultrashort optical pulses to trigger a reaction in solution and using time‐resolved X‐ray diffraction (scattering) to interrogate the structural changes in the molecules, time‐resolved X‐ray liquidography (TRXL) is a direct tool for probing structural dynamics for chemical reactions in solution. TRXL can provide direct structural information that is difficult to extract from ultrafast optical spectroscopy, such as the time dependence of bond lengths and angles of all molecular species including short‐lived intermediates over a wide range of times, from picoseconds to milliseconds. TRXL elegantly complements ultrafast optical spectroscopy because the diffraction signals are sensitive to all chemical species simultaneously and the diffraction signal from each chemical species can be quantitatively calculated from its three‐dimensional atomic coordinates and compared with experimental TRXL data. Since X‐rays scatter from all the atoms in the solution sample, solutes as well as the solvent, the analysis of TRXL data can provide the temporal behavior of the solvent as well as the structural progression of all the solute molecules in all the reaction pathways, thus providing a global picture of the reactions and accurate branching ratios between multiple reaction pathways. The arrangement of the solvent around the solute molecule can also be extracted. This review summarizes recent developments in TRXL, including technical innovations in synchrotron beamlines and theoretical analysis of TRXL data, as well as several examples from simple molecules to an organometallic complex, nanoparticles, and proteins in solution. Future potential applications of TRXL in femtosecond studies and biologically relevant molecules are also briefly mentioned.