Low-dose Electron Diffraction Research Articles

Structure solution and refinement of beam-sensitive nano-crystals

Radiation sensitive materials are among the most difficult materials to study, even more so if they exist only as nanometer-sized particles, where their size is either intentional because of enhanced properties at the nano-scale or it is unintentional because it is impossible to obtain bigger particles of the same structure. In both cases characterization methods need to be optimized to get the most information out of these particles before the radiation damages them to a point where their structure is altered. When the particles are crystallized, both characteristics, the small size and the beam sensitivity, call for electron diffraction as a privileged investigation tool. The strong interaction of electrons (as compared to X-rays) with matter allows single crystal diffraction experiments on nanometer-sized crystals and for the same amount of beam damage, electron diffraction yields more information than X-rays. These inherent advantages of electron diffraction are optimized in the recently developed low-dose electron diffraction tomography (LD-EDT) by minimizing the necessary dose for a complete data collection. In this contribution we show that in some cases even doses as low as 2 e-/Ų can induce damage in crystal structures that inhibit a correct structure refinement. However, by LD-EDT we can obtain data using extremely low doses that don’t alter the structure which make it then possible not only to solve crystal structures but also to refine them using dynamical diffraction theory. Here a synthetic oxide containing volatile Na and a metal-organic framework are given as examples. A dynamical refinement of the structures is possible with data sets requiring a dose of less than 0.15 e-/Ų.

Dose symmetric electron diffraction tomography (DS-EDT): Implementation of a dose-symmetric tomography scheme in 3D electron diffraction

Beam sensitive nanomaterials such as zeolites or metal-organic frameworks (MOF) represent a great challenge for crystallographic structure determination and refinement. The strong electron-matter interaction and the high spatial resolution achievable make electron diffraction the technique of choice for particles of sizes below a micrometer and many different 3-dimensional electron diffraction (3D ED) techniques have been developed in recent years. Nevertheless, beam sensitivity of the samples can lead to the crystal structure being damaged during the data acquisition impeding the determination of its structure. A simple way to reduce beam damage is to lower the dose during the experiment. However, this implies weaker diffraction intensities which can become problematic for the exploitation of the data.In order to obtain complete data sets with strong intensities without damaging the crystals, we developed the dose symmetric electron diffraction tomography (DS-EDT) method, combining the low-dose electron diffraction tomography (LD-EDT) technique with the dose-symmetric tomography scheme known from cryo-EM. In order to reduce the dose on an individual crystal and still obtain enough data for a structure solution and refinement, we partition the dose over several crystals. The individual datasets are then merged in order to achieve the necessary completeness. On two test structures we first show that merging of data from small domains of the reciprocal space is indeed sufficient to obtain reliable data for structure solution and refinement. Second, we show on the beam sensitive manganese formate that high-quality data can be obtained on a few frames while the frames that have suffered from beam damage can still be used to determine the orientation matrix and the unit cell of the crystals. The results from the dynamical refinement on the obtained data show a high accuracy of the atom positions. In this way, DS-EDT can reduce the total dose on an individual crystal by an order of magnitude with respect to the already very dose-efficient LD-EDT.

Direct observation of crystal degradation behaviour in porous crystals under low-dose electron diffraction conditions.

The quantification of electron beam damage in crystalline porous materials has been investigated under low-dose electron irradiation conditions. As a result of the systematic quantitative analysis of time-course changes in electron diffraction patterns, it was found that the unoccupied volume in the MOF crystal is a crucial factor for electron beam resistance.

Structure determination of intermetallic phases in bulk Al alloys by 3D electron diffraction tomography

Secondary phases in bulk metallic samples are difficult to characterize by conventional X-ray diffraction because the diffracted intensities are dominated by the contribution of the bulk material. Electron diffraction provides a better spatial resolution and one can obtain single crystal diffraction data from submicron sized precipitates. In this work we show that 3D electron diffraction tomography can yield diffraction data sets suitable for ab initio structure solution. We apply the recently proposed low-dose electron diffraction tomography method to 3 different phases in Al-based alloys: θ’-Al 2 Cu, Al 6 Fe and Al 4.5 FeSi. The structures of these phases were unambiguously determined even though there are other phases with similar chemical compositions and EDS analysis is not sufficient to distinguish them. • Intermetallics’ chemical composition can be too similar to be distinguished by EDS. • Intermetallics’ unit cell parameters can be too similar to be distinguished by SAED. • Precipitate phases can be unambiguously identified by 3D electron diffraction. • 3 phases of increasing complexity are identified.

Low-Dose Electron Crystallography: Structure Solution and Refinement

There is a wealth of materials that are beam sensitive and only exist in nanometric crystals, because the growth of bigger crystals is either impossible or so complicated that it is not reasonable to spend enough time and resources to grow big crystals before knowing their potential for research or applications. This difficulty is encountered in minerals, zeolites, metal-organic frameworks or molecular crystals, including pharmaceuticals and biological crystals. In order to study these crystals a structure determination method for beam sensitive crystals of nanometric size is needed. The nanometric size makes them destined for electron diffraction, since electrons interact much more strongly with matter than X-rays or neutrons. In addition, for the same amount of beam damage, electron diffraction yields more information than X-rays. The recently developed low-dose electron diffraction tomography (LD-EDT) not only combines the advantages inherent in electron diffraction, but is also optimized for minimizing the electron dose used for the data collection. The data quality is high, allowing not only the solution of complex unknown structures, but also their refinement taking into account the dynamical diffraction effects. Here we present several examples of crystals solved and refined by this method. The range of the crystals presented includes two synthetic oxides, Sr5CuGe9O24 and (Na2/3Mn1/3)3Ge5O12, a natural mineral (bulachite), and a metal organic framework (Mn-formiate). The dynamical refinement can be successfully performed on data sets that needed less than 0.1 e−/Å2 for the entire data set.

Low-dose electron diffraction tomography (LD-EDT) in TEM: application on a hydrated Al arsenate mineral

Low-dose electron diffraction tomography (LD-EDT) in TEM: application on a hydrated Al arsenate mineral

Three different Ge environments in a new Sr5CuGe9O24 phase synthesized at high pressure and high temperature.

In the framework of expanding the range of copper-based compounds in the pyroxene family, we have synthesized at high pressure and high temperature a powder containing a mixture of a new phase with stoichiometry Sr5CuGe9O24 having two identified impurity phases. Electron crystallography showed that the new phase crystallizes in the monoclinic space group P2/c, with unit-cell parameters a = 11.8 Å, b = 8.1 Å, c = 10.3 Å and β = 101.3°. We applied the recently developed low-dose electron diffraction tomography method to solve the structure by direct methods. The obtained structure model contains all 9 independent cation positions and all 13 oxygen positions. A subsequent refinement against powder X-ray diffraction data ascertained the high quality of the structure solution, in particular, the unusual structural arrangement that there are three different environments for Ge in this phase.

Bulachite, [Al6(AsO4)3(OH)9(H2O)4]⋅2H2O from Cap Garonne, France: Crystal structure and formation from a higher hydrate

AbstractBulachite specimens from Cap Garonne, France, comprise two intimately mixed hydrated aluminium arsenate minerals with the same Al:As ratio of 2:1 and with different water contents. The crystal structures of both minerals have been solved using data from low-dose electron diffraction tomography combined with synchrotron powder X-ray diffraction. One of the minerals has the same powder X-ray diffraction pattern (PXRD) as for published bulachite. It has orthorhombic symmetry, space group Pnma with unit-cell parameters a = 15.3994(3), b = 17.6598(3), c = 7.8083(1) Å and Z = 4, with the formula [Al6(AsO4)3(OH)9(H2O)4]⋅2H2O. The second mineral is a higher hydrate with composition [Al6(AsO4)3(OH)9(H2O)4]⋅8H2O. It has the same Pnma space group and unit-cell parameters a = 19.855(4), b = 17.6933(11) and c = 7.7799(5) Å i.e. almost the same b and c parameters but a much larger a parameter. The structures are based on polyhedral layers, parallel to (100), of composition [Al6(AsO4)3(OH)9(H2O)4] and with H-bonded H2O between the layers. The layers contain [001] spiral chains of edge-shared octahedra, decorated with corner connected AsO4 tetrahedra that are the same as in the mineral liskeardite. The spiral chains are joined together by octahedral edge-sharing to form layers parallel to (100). Synchrotron PXRD patterns collected at different temperatures during heating of the specimen show that the higher-hydrate mineral starts transforming to bulachite when heated to 50°C, and the transformation is complete between 75 and 100°C.

Transmission electron microscopy of organic-inorganic hybrid perovskites: myths and truths

Organic-inorganic hybrid perovskites (OIHPs) have attracted extensive research interest as a promising candidate for efficient and inexpensive solar cells. Transmission electron microscopy (TEM) characterizations that can benefit the fundamental understanding and the degradation mechanism are widely used for these materials. However, their sensitivity to the electron beam illumination and hence structural instabilities usually prevent us from obtaining the intrinsic information or even lead to significant artifacts. Here, we systematically investigate the structural degradation behaviors under different experimental factors to reveal the optimized conditions for TEM characterizations of OIHPs by using low-dose electron diffraction and imaging techniques. We find that a low temperature (−180 °C) does not slow down the beam damage but instead induces a rapid amorphization for OIHPs. Moreover, a less severe damage is observed at a higher accelerating voltage. The beam-sensitivity is found to be facet-dependent that a (1 0 0) exposed CH3NH3PbI3 (MAPbI3) surface is more stable than a (0 0 1) surface. With these guidance, we successfully acquire the atomic structure of pristine MAPbI3 and identify the characterization window that is very narrow. These findings are helpful to guide future electron microscopy characterizations of these beam-sensitive materials, which are also useful for finding strategies to improve the stability and performance of the perovskite solar cells.

Low-dose electron diffraction tomography (LD-EDT) solves the structure of a new (Na2/3Mn1/3)2Mn3Ge3O12 phase synthesized at high pressure and high temperature

Low-dose electron diffraction tomography (LD-EDT) solves the structure of a new (Na_2/3Mn_1/3)₂Mn₃Ge₃O₁₂ phase synthesized at high pressure and high temperature

Low-dose electron diffraction tomography (LD-EDT)

A new electron diffraction tomography method is presented that is aimed to enable high performance electron crystallography experiments on beam sensitive materials using a standard TEM without any special equipment. Low-dose electron diffraction tomography minimizes the electron dose necessary for obtaining data sets suitable for structure solution by irradiating the crystal exclusively during the acquisition of the diffraction patterns.The performance of the method is successfully tested on two model structures, a complex oxide Sr5CuGe9O24 and the beam sensitive metal-organic framework (MOF) of manganese formiate. Even when the limited lifetime of a beam sensitive material only allows obtaining a data set of rather low completeness, the data quality is high enough for the structures to be solved to a high precision.Low-dose electron diffraction tomography is easy to implement and doesn't require any special equipment or lengthy calibration processes, making it accessible to a large number of scientists.

Applications of the highly efficient low-dose electron diffraction tomography

Applications of the highly efficient low-dose electron diffraction tomography

Low-dose electron diffraction tomography

Low-dose electron diffraction tomography

Single electrospun PLLA and PCL polymer nanofibers: Increased molecular orientation with decreased fiber diameter

Electrospinning has become a widely-used method for fabricating polymer nanofibers for various applications including filtration, drug delivery, and tissue engineering. Due to the high extensional forces during the electrospinning process, and the rapid crystallization and solidification during solvent evaporation, molecular orientation may develop within the resulting fibers. The properties of electrospun fibers are expected to be sensitive to level of orientation in the fibers. Various reports have shown an increased modulus with decreased fiber diameter, and molecular orientation has been used to explain this trend. However, there have been relatively few studies of the detailed relationship between fiber diameter and molecular orientation, especially at the single fiber level. Here we report a quantitative study of the orientation in individual electrospun poly(caprolactone) (PCL) and poly(l-lactic acid) (PLLA) fibers using low-dose electron microscopy and diffraction techniques. Our results confirmed that for electrospun fibers of PCL and PLLA processed under similar experimental conditions, the molecular orientation decreased as the fiber diameter increased. The extent of orientation remained high for quite large fiber diameters, with azimuthal orientation of 20° seen up to ∼500 nm for PCL and ∼2000 nm for PLLA.

Supramolecular organization of a H-bonded perylene bisimide organogelator determined by transmission electron microscopy, grazing incidence X-ray diffraction and polarized infra-red spectroscopy.

An organogelator based on a N,N'-substituted H-bonding perylenebisimide (PBI-C10) self-assembles to form either a green J-type (form I) or a red H-type (form II) aggregate structure. The molecular packing of both polymorphs was determined from a combination of Transmission Electron Microscopy (TEM) (low dose electron diffraction and high resolution), Grazing incidence X-ray diffraction and polarized infrared spectroscopy. To that aim, highly oriented films have been prepared by mechanical rubbing at controlled film temperature and DFT calculations were performed to identify representative vibrational IR bands and their associated polarizations. H-Bonding between amides generates either a rectangular columnar phase (form I) in the dried gel or a hexagonal packing of supramolecular 21/1 helices with a long period of 97 Å (form II) in annealed thin films. In aligned films of form I, polarized FTIR spectroscopy helps determine the orientation of both intermolecular H-bonds and the PBI core with respect to the substrate. In form II, PBI-C10 molecules assemble into pairs to form off-centered 21/1 helices whose helical axis is made of strongly H-bonded amides. TEM investigations show that three 21/1 helices are packed in a frustrated trigonal structure formed by H-bonding. The Form I → Form II transformation implies a redistribution of a single population of strong intra-columnar H-bonds between amides in form I to a mixture of strong and weak H-bonds in the supramolecular helices, the strong H-bonds forming the spine of the helices.

Monolayer-to-thin-film transition in supramolecular assemblies: the role of topological protection.

The ability to control the transition from a two-dimensional (2D) monolayer to the three-dimensional (3D) molecular structure in the growth of organic layers on surfaces is essential for the production of functional thin films and devices. This has, however, proved to be extremely challenging, starting from the currently limited ability to attain a molecular scale characterization of this transition. Here, through innovative application of low-dose electron diffraction and aberration-corrected transmission electron microscopy (acTEM), combined with scanning tunneling microscopy (STM), we reveal the structural changes occurring as film thickness is increased from monolayer to tens of nanometers for supramolecular assembly of two prototypical benzenecarboxylic acids - terephthalic acid (TPA) and trimesic acid (TMA) - on graphene. The intermolecular hydrogen bonding in these molecules is similar and both form well-ordered monolayers on graphene, but their structural transitions with film thickness are very different. While the structure of TPA thin films varies continuously towards the 3D lattice, TMA retains its planar monolayer structure up to a critical thickness, after which a transition to a polycrystalline film occurs. These distinctive structural evolutions can be rationalized in terms of the topological differences in the 3D crystallography of the two molecules. The templated 2D structure of TPA can smoothly map to its 3D structure through continuous molecular tilting within the unit cell, whilst the 3D structure of TMA is topologically distinct from its 2D form, so that only an abrupt transition is possible. The concept of topological protection of the 2D structure gives a new tool for the molecular design of nanostructured films.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector.

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼ 0.013 e(-) Å(-2) s(-1)) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014).

Analysis of Electron Beam Damage of Crystalline Pharmaceutical Materials by Transmission Electron Microscopy

We have studied the impact of transmission electron microscopy (TEM) and low dose electron diffraction on ten different crystalline pharmaceutical compounds, covering a diverse chemical space and with differing physical properties. The aim was to establish if particular chemical moieties were more susceptible to damage within the electron beam. We have measured crystalline diffraction patterns for each and indexed nine out of ten of them. Characteristic electron dosages are reported for each material, with no apparent correlation between chemical structure and stability within the electron beam. Such low dose electron diffraction protocols are suitable for the study of pharmaceutical compounds.

Partial oxidation as a rational approach to kinetic control in bioinspired magnetite synthesis.

Biological systems show impressive control over the shape, size and organization of mineral structures, which often leads to advanced physical properties that are tuned to the function of these materials. Such control is also found in magnetotactic bacteria, which produce-in aqueous medium and at room temperature-magnetite nanoparticles with precisely controlled morphologies and sizes that are generally only accessible in synthetic systems with the use of organic solvents and/or the use of high-temperature methods. The synthesis of magnetite under biomimetic conditions, that is, in water and at room temperature and using polymeric additives as control agents, is of interest as a green production method for magnetic nanoparticles. Inspired by the process of magnetite biomineralization, a rational approach is taken by the use of a solid precursor for the synthesis of magnetite nanoparticles. The conversion of a ferrous hydroxide precursor, which we demonstrate with cryo-TEM and low-dose electron diffraction, is used to achieve control over the solution supersaturation such that crystal growth can be regulated through the interaction with poly-(α,β)-dl-aspartic acid, a soluble, negatively charged polymer. In this way, stable suspensions of nanocrystals are achieved that show remanence and coercivity at the size limit of superparamagnetism, and which are able to align their magnetic moments forming strings in solution as is demonstrated by cryo-electron tomography.

Three-Dimensional Structure of P3HT Assemblies in Organic Solvents Revealed by Cryo-TEM

Poly(3-hexylthiophene) (P3HT) assemblies in vitrified organic solvents were visualized at nanometer scale resolution by cryo-transmission electron microscopy, low dose electron diffraction, and cryo-tomography revealing a three-dimensional lamellar structure formed by the stacking of the conjugated backbones of P3HT with a distance of 1.7 nm and increased order in the bulk of the nanowire. This combination of techniques reveals local structures in dispersion and the condensed state that play a crucial role in the performance of organic electronic devices.