Effects of coating spherical iron oxide nanoparticles.

We investigate the effect of several coatings applied in biomedical applications to iron oxide nanoparticles on the size, structure and composition of the particles. The four structural techniques employed - TEM, DLS, VSM, SAXS and EXAFS - show no significant effects of the coatings on the spherical shape of the bare nanoparticles, the average sizes or the local order around the Fe atoms. The NPs coated with hydroxylmethylene bisphosphonate or catechol have a lower proportion of magnetite than the bare and citrated ones, raising the question whether the former are responsible for increasing the valence state of the oxide on the NP surfaces and lowering the overall proportion of magnetite in the particles. VSM measurements show that these two coatings lead to a slightly higher saturation magnetization than the citrate. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.

Fullrmc, a rigid body Reverse Monte Carlo modeling package enabled with machine learning and artificial intelligence.

A new Reverse Monte Carlo (RMC) package "fullrmc" for atomic or rigid body and molecular, amorphous, or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython, C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with a set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modeling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. In addition, fullrmc provides a unique way with almost no additional computational cost to recur a group's selection, allowing the system to go out of local minimas by refining a group's position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group.

Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of DMPC phase transitions.

Neutron scattering techniques have been employed to investigate 1,2-dimyristoyl-sn -glycero-3-phosphocholine (DMPC) membranes in the form of multilamellar vesicles (MLVs) and deposited, stacked multilamellar-bilayers (MLBs), covering transitions from the gel to the liquid phase. Neutron diffraction was used to characterise the samples in terms of transition temperatures, whereas elastic incoherent neutron scattering (EINS) demonstrates that the dynamics on the sub-macromolecular length-scale and pico- to nano-second time-scale are correlated with the structural transitions through a discontinuity in the observed elastic intensities and the derived mean square displacements. Molecular dynamics simulations have been performed in parallel focussing on the length-, time- and temperature-scales of the neutron experiments. They correctly reproduce the structural features of the main gel-liquid phase transition. Particular emphasis is placed on the dynamical amplitudes derived from experiment and simulations. Two methods are used to analyse the experimental data and mean square displacements. They agree within a factor of 2 irrespective of the probed time-scale, i.e. the instrument utilized. Mean square displacements computed from simulations show a comparable level of agreement with the experimental values, albeit, the best match with the two methods varies for the two instruments. Consequently, experiments and simulations together give a consistent picture of the structural and dynamical aspects of the main lipid transition and provide a basis for future, theoretical modelling of dynamics and phase behaviour in membranes. The need for more detailed analytical models is pointed out by the remaining variation of the dynamical amplitudes derived in two different ways from experiments on the one hand and simulations on the other.

Liquid structure of dibutyl sulfoxide.

We present experimental (X-ray diffraction) data on the structure of liquid dibutyl sulfoxide at 320 K and rationalise the data by means of molecular dynamics simulations. Not unexpectedly, DBSO bearing a strong dipolar moiety and two medium length, apolar butyl chains, this compound was characterised by a distinct degree of polar vs. apolar structural differentiation at the nm spatial scale, which was fingerprinted by a low Q peak in its X-ray diffraction pattern. Similar to, but to a larger extent than its shorter chain family members (such as DMSO), DBSO was also characterised by an enhanced dipole-dipole correlation, which was responsible for a moderate Kirkwood correlation factor as well as for the self-association detected in this compound. We show, however, that the supposedly relevant hydrogen bonding correlations between oxygen and the butyl chain hydrogens are of a limited extent only, and only in the case of α-hydrogens is an appreciable indication of the existence of such an interaction found, albeit this turned out to be a mere consequence of the strong dipole-dipole correlation.

Effect of water on the structure of a prototype ionic liquid.

The influence of water on the structure of a prototype ionic liquid (IL) 1-octyl-3-methylimidazolium tetrafluoroborate (C8mimBF4) is examined in the IL-rich regime using high-energy X-ray diffraction (HEXRD) and molecular dynamics (MD) simulations. A many-body polarizable force field APPLE&P was developed for C8mimBF4-water mixture. It predicts structure factors of pure IL and IL-water mixture in excellent agreement with the HEXRD experiments. The MD results provide detailed insights into the structural changes from the partial structure factors, 2-D projections of the simulation box and 3-D distribution functions. Water partitioning with IL and its competition with BF4(-) for complexing the imidazolium rings was examined. The added water molecules occupy a diffuse coordination shell around the imidazolium ring but are not present around the alkyl tail. The strong coordination of the fluorine atoms of the BF4(-) anions to the imidazolium ring is not significantly changed by the addition of water. A complementary packing of water and imidazolium around BF4(-) was found. These results are consistent with the very small differences in the average structure between the pure IL and the mixture.

Nanoscale heterogeneity in alkyl-methylimidazolium bromide ionic liquids.

High-energy x-ray diffraction measurements and atomistic molecular dynamics (AMD) numerical simulations have been carried out on 1-alkyl-3-methylimidazolium bromide ionic liquids, C(n)mimBr, with n = 2, 4, and 6. Excellent agreement between experiment and simulation is obtained, including the region of the low-Q peak that has proved problematic in previous work in the literature. In the partial structure analysis of the AMD results, a distinct peak develops at the leading edge of the ring-ring pair distribution function and shifts to lower r with increasing alkyl chain length, indicating that the preferential parallel and antiparallel alignment of neighboring cation rings plays a larger role with increasing chain length. The ring-ring, anion-anion, and ring-anion partial structure factors are dominated by strong charge-ordering peaks around 1.1 Å(-1), corresponding to a distance between neighboring polar entities of D(2) = 5.7 Å. In contrast, the tail-tail S(Q) is dominated by the low-Q peak that rises and moves to lower Q with increasing chain length; the length scale of this structural heterogeneity D(1) increases from about 10 Å in C(2)mimBr to 14.3 Å in C(4)mimBr and 18.8 Å in C(6)mimBr. Both the length scale of the structural heterogeneity and its anomalous temperature dependence in the C(n)mimBr liquids studied here show considerable similarity to results in the literature for C(n)mimPF(6) liquids, indicating a remarkable insensitivity to the form and size of the anion. Our results are consistent with the concept of nanoscale heterogeneity with small, crystal-like moieties.

Probing the Atomic-Scale Structure of Amorphous Aluminum Oxide Grown by Atomic Layer Deposition.

Atomic layer deposition (ALD) is a well-established technique for depositing nanoscale coatings with pristine control of film thickness and composition. The trimethylaluminum (TMA) and water (H2O) ALD chemistry is inarguably the most widely used and yet to date, we have little information about the atomic-scale structure of the amorphous aluminum oxide (AlOx) formed by this chemistry. This lack of understanding hinders our ability to establish process-structure-property relationships and ultimately limits technological advancements employing AlOx made via ALD. In this work, we employ synchrotron high-energy X-ray diffraction (HE-XRD) coupled with pair distribution function (PDF) analysis to characterize the atomic structure of amorphous AlOx ALD coatings. We combine ex situ and in operando HE-XRD measurements on ALD AlOx and fit these experimental data using stochastic structural modeling to reveal variations in the Al-O bond length, Al and O coordination environment, and extent of Al vacancies as a function of growth conditions. In particular, the local atomic structure of ALD AlOx is found to change with the substrate and number of ALD cycles. The observed trends are consistent with the formation of bulk Al2O3 surrounded by an O-rich surface layer. We deconvolute these data to reveal atomic-scale structural information for both the bulk and surface phases. Overall, this work demonstrates the usefulness of HE-XRD and PDF analysis in improving our understanding of the structure of amorphous ALD thin films and provides a pathway to evaluate how process changes impact the structure and properties of ALD films.

Structure of a prototypic ionic liquid: ethyl-methylimidazolium bromide.

High-energy X-ray diffraction measurements have been carried out on 1-ethyl-3-methylimidazolium bromide and complemented with molecular-dynamics simulations. Because the structure of the corresponding crystal is known, both the liquid and the crystal phases are simulated numerically. The liquid structure factor is dominated by an intense peak at 1.7 A(-1), associated mainly with the packing of the anions around the large cations. Analysis of the real-space correlations of the liquid shows that the Br(-) ions are distributed more symmetrically around the cation ring and move closer to the ring atoms compared with the crystal. Although the distribution of the anions around the cation in the first coordination shell of the liquid exhibits clear analogies with the crystal, the cation-cation partial distribution function of the liquid shows a significant component with lower distances between ring centers, with some pairs coming as close as 3.5 A in either parallel or antiparallel configurations. Finally, the presence of topological short-range order and charge ordering in the liquid is clearly demonstrated.