Gold nanoparticles obtained by ns-pulsed laser ablation in liquids (ns-PLAL) are arranged in the form of fractal clusters

Gold nanoparticles (AuNPs), synthesized by ns-pulsed laser ablation in liquid (ns-PLAL) in the absence of any capping agents, are potential model systems to study the interactions with biological structures unencumbered by interference from the presence of stabilizers and capping agents. However, several aspects of the physics behind these AuNPs solutions deserve a detailed investigation. The structure in solution of ns-PLAL-synthesized AuNPs was investigated in solution by means of small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS). Furthermore, the (dried) NPs have been examined using TEM. The analysis of the SAXS curve shows the presence of a large number of small aggregates with a fractal structure stabilized by strong long-range repulsive interactions. Fitting of the SAXS curve to a suitable “fractal model” allows the estimation of the features of the fractal including the fractal dimension d = 1.9. The latter allows to estimate the fraction of light scattered by fractals of different sizes and thus permits a fair comparison between the DLS and TEM data. Here, a stable abundant population of fractal clusters is reported reflecting a mechanism where primary AuNPs (size 7.6 nm) are forced to aggregate forming clusters during the collapse of the cavitation bubble. When these clusters are released in the aqueous phase, their large negative charge builds up repulsive interactions that prevent cluster-cluster aggregation imparting colloidal stability.

Z-score to evaluate the absolute quality of macromolecular models based on SAXS data

Small-angle X-ray scattering (SAXS) is a highly popular technique to assess the native three-dimensional structure of biological macromolecules in solution. Here we introduce a statistical criterion, Z-score, as a novel quality measure of SAXS-based structural models which positively correlates with data quality. We propose that, besides a goodness-of-fit (GOF) measure such as reduced χ2, the Z-score reflecting the ability of a given SAXS curve to differentiate between possible models should always be reported.

Modeling of Polymer Structure with the Use of SAXSDAT Computer Program

The most important structural parameters of semicrystalline polymers can be determined by modeling of their structure and best fitting of a theoretical intensity distribution calculated for the assumed model to the experimental SAXS curve. This paper presents a module of a computer program SAXSDAT dedicated to such calculations.

Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale

This paper describes a new and simple method to determine the molecular weight of proteins in dilute solution, with an error smaller than ∼10%, by using the experimental data of a single small-angle X-ray scattering (SAXS) curve measured on a relative scale. This procedure does not require the measurement of SAXS intensity on an absolute scale and does not involve a comparison with another SAXS curve determined from a known standard protein. The proposed procedure can be applied to monodisperse systems of proteins in dilute solution, either in monomeric or multimeric state, and it has been successfully tested on SAXS data experimentally determined for proteins with known molecular weights. It is shown here that the molecular weights determined by this procedure deviate from the known values by less than 10% in each case and the average error for the test set of 21 proteins was 5.3%. Importantly, this method allows for an unambiguous determination of the multimeric state of proteins with known molecular weights.

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

Easy-to-use indirect Fourier transformation routines for evaluation of slit-length-smeared SAXS curves of polystyrene in solution

Two easy-to-use indirect Fourier-transformation routines for the evaluation of slit-length-smeared SAXS curves of polystyrene in solution are demonstrated. For approximation of the SAXS curve, analytically transformable Gaussian and Lorentzian functions are chosen. The nonlinear least-squares fit is transformed to a linear one by specifying fixed non-linear coefficients. The fit is constrained by allowing only positive linear coefficients. The range over which nonlinear coefficients have to be specified can be easily obtained from the SAXS curve. An exact specification of this range is unnecessary for the fit. The method allows direct and clear control of the indirect Fourier transformation.

Structure of Soluble Silicates

ABSTRACTSmall angle x-ray scattering (SAXS) is the technique of choice for the determination of structure on the 10–1000Å scale. We have used this technique to study the growth and topology of the macromolecules which precede gelation in several chemical systems used in sol-gel glass technology. The results show that branched polymers, as opposed to colloids, are formed. The alcoholic silica system is akin to organic systems where gelation occurs through growth and crosslinking of chain molecules. Data are reported from both the Porod and Guinier regions of the SAXS curve and these data are interpreted in terms of geometrical structures predicted by various disorderly growth processes. The results indicate that the degree of crosslinking can be controlled by catalytic conditions. The degree of crosslinking may, in turn, control phase separation and processability to a dense glass.