Enabling near-atomic-scale analysis of frozen water

Towards Establishing Best Practice in the Analysis of Hydrogen and Deuterium by Atom Probe Tomography

As hydrogen is touted as a key player in the decarbonization of modern society, it is critical to enable quantitative hydrogen (H) analysis at high spatial resolution and, if possible, at the atomic scale. H has a known deleterious impact on the mechanical properties (strength, ductility, toughness) of most materials that can hinder their use as part of the infrastructure of a hydrogen-based economy. Enabling H mapping including local hydrogen concentration analyses at specific microstructural features is essential for understanding the multiple ways that H affect the properties of materials including embrittlement mechanisms and their synergies. In addition, spatial mapping and quantification of hydrogen isotopes is essential to accurately predict tritium inventory of future fusion power plants thus ensuring their safe and efficient operation. Atom probe tomography (APT) has the intrinsic capability to detect H and deuterium (D), and in principle the capacity for performing quantitative mapping of H within a material's microstructure. Yet, the accuracy and precision of H analysis by APT remain affected by complex field evaporation behavior and the influence of residual hydrogen from the ultrahigh vacuum chamber that can obscure the signal of H from within the material. The present article reports a summary of discussions at a focused workshop held at the Max-Planck Institute for Sustainable Materials in April 2024. The workshop was organized to pave the way to establishing best practices in reporting APT data for the analysis of H. We first summarize the key aspects of the intricacies of H analysis by APT and then propose a path for better reporting of the relevant data to support interpretation of APT-based H analysis in materials.

Nanoscale Analysis of Frozen Water by Atom Probe Tomography Using Graphene Encapsulation and Cryo-Workflows

There has been an increasing interest in atom probe tomography (APT) to characterize hydrated and biological materials. A major benefit of APT compared to microscopy techniques more commonly used in biology is its combination of outstanding three-dimensional (3D) spatial resolution and mass sensitivity. APT has already been successfully used to characterize biominerals, revealing key structural information at the atomic scale, however there are many challenges inherent to the analysis of soft hydrated materials. New preparation protocols, often involving specimen preparation and transfer at cryogenic temperature, enable APT analysis of hydrated materials and have the potential to enable 3D atomic scale characterization of biological materials in the near-native hydrated state. In this study, samples of pure water at the tips of tungsten needle specimens were prepared at room temperature by graphene encapsulation. A comparative study was conducted where specimens were transferred at either room temperature or cryo-temperature and analyzed by APT by varying the flight path and pulsing mode. The differences between the analysis workflows are presented along with recommendations for future studies, and the compatibility between graphene coating and cryogenic workflows is demonstrated.

Analysis of Water Ice in Nanoporous Copper Needles Using Cryo Atom Probe Tomography

The application of atom probe tomography (APT) to frozen liquids is limited by difficulties in specimen preparation. Here, we report on the use of nanoporous Cu needles as a physical framework to hold water ice for investigation using APT. Nanoporous Cu needles are prepared by electropolishing and dealloying Cu-Mn matchstick precursors. Cryogenic scanning electron microscopy and focused ion beam milling reveal a hierarchical, dendritic, highly wettable microstructure. The atom probe mass spectrum is dominated by peaks of Cu+ and H(H2O)n+ up to n ≤ 3, and the reconstructed volume shows the protrusion of a Cu ligament into an ice-filled pore. The continuous Cu ligament network electrically connects the apex to the cryostage, leading to an enhanced electric field at the apex and increased cooling, both of which simplify the mass spectrum compared to previous reports.

Nanoporous Gold Thin Films as Substrates to Analyze Liquids by Cryo-atom Probe Tomography

Cryogenic atom probe tomography (cryo-APT) is being developed to enable nanoscale compositional analyses of frozen liquids. Yet, the availability of readily available substrates that allow for the fixation of liquids while providing sufficient strength to their interface is still an issue. Here, we propose the use of 1-2-µm-thick binary alloy film of gold-silver sputtered onto flat silicon, with sufficient adhesion without an additional layer. Through chemical dealloying, we successfully fabricate a nanoporous substrate, with an open-pore structure, which is mounted on a microarray of Si posts by lift-out in the focused-ion beam system, allowing for cryogenic fixation of liquids. We present cryo-APT results obtained after cryogenic sharpening, vacuum cryo-transfer, and analysis of pure water on the top and inside the nanoporous film. We demonstrate that this new substrate has the requisite characteristics for facilitating cryo-APT of frozen liquids, with a relatively lower volume of precious metals. This complete workflow represents an improved approach for frozen liquid analysis, from preparation of the films to the successful fixation of the liquid in the porous network, to cryo-APT.

Quasi-"In Situ" Analysis of the Reactive Liquid-Solid Interface during Magnesium Corrosion Using Cryo-Atom Probe Tomography

The early stages of corrosion occurring at liquid-solid interfaces control the evolution of the material's degradation process, yet due to their transient state, their analysis remains a formidable challenge. Here corrosion tests are performed on a MgCa alloy, a candidate material for biodegradable implants using pure water as a model system. The corrosion reaction is suspended by plunge freezing into liquid nitrogen. The evolution of the early-stage corrosion process on the nanoscale by correlating cryo-atom probe tomography (APT) with transmission-electron microscopy (TEM) and spectroscopy, is studied. The outward growth of Mg hydroxide Mg(OH)2 and the inward growth of an intermediate corrosion layer consisting of hydrloxides of different compositions, mostly monohydroxide Mg(OH) instead of the expected MgO layer, are observed. In addition, Ca partitions to these newly formed hydroxides and oxides. Density-functional theory calculations suggest a domain of stability for this previously experimental unreported Mg(OH) phase. This new approach and these new findings advance the understanding of the early stages of magnesium corrosion, and in general reactions and processes at liquid-solid interfaces, which can further facilitate the development of corrosion-resistant materials or better control of the biodegradation rate of future implants.

A Versatile and Reproducible Cryo-sample Preparation Methodology for Atom Probe Studies

Repeatable and reliable site-specific preparation of specimens for atom probe tomography (APT) at cryogenic temperatures has proven challenging. A generalized workflow is required for cryogenic specimen preparation including lift-out via focused ion beam and in situ deposition of capping layers, to strengthen specimens that will be exposed to high electric field and stresses during field evaporation in APT and protect them from environment during transfer into the atom probe. Here, we build on existing protocols and showcase preparation and analysis of a variety of metals, oxides, and supported frozen liquids and battery materials. We demonstrate reliable in situ deposition of a metallic capping layer that significantly improves the atom probe data quality for challenging material systems, particularly battery cathode materials which are subjected to delithiation during the atom probe analysis itself. Our workflow design is versatile and transferable widely to other instruments.

The Fate of Water in Hydrogen-Based Iron Oxide Reduction

Gas-solid reactions are important for many redox processes that underpin the energy and sustainability transition. The specific case of hydrogen-based iron oxide reduction is the foundation to render the global steel industry fossil-free, an essential target as iron production is the largest single industrial emitter of carbon dioxide. This perception of gas-solid reactions has not only been limited by the availability of state-of-the-art techniques which can delve into the structure and chemistry of reacted solids, but one continues to miss an important reaction partner that defines the thermodynamics and kinetics of gas phase reactions: the gas molecules. In this investigation, cryogenic-atom probe tomography is used to study the quasi in situ evolution of iron oxide in the solid and gas phases of the direct reduction of iron oxide by deuterium gas at 700°C. So far several unknown atomic-scale characteristics are observed, including, D2 accumulation at the reaction interface; formation of a core (wüstite)-shell (iron) structure; inbound diffusion of D through the iron layer and partitioning of D among phases and defects; outbound diffusion of oxygen through the wüstite and/or through the iron to the next free available inner/outer surface; and the internal formation of heavy nano-water droplets at nano-pores.

In Situ Sputtering From the Micromanipulator to Enable Cryogenic Preparation of Specimens for Atom Probe Tomography by Focused-Ion Beam

Workflows have been developed in the past decade to enable atom probe tomography analysis at cryogenic temperatures. The inability to control the local deposition of the metallic precursor from the gas-injection system (GIS) at cryogenic temperatures makes the preparation of site-specific specimens by using lift-out extremely challenging in the focused-ion beam. Schreiber et al. exploited redeposition to weld the lifted-out sample to a support. Here, we build on their approach to attach the region-of-interest and additionally strengthen the interface with locally sputtered metal from the micromanipulator. Following standard focused-ion beam annular milling, we demonstrate atom probe analysis of Si in both laser pulsing and voltage mode, with comparable analytical performance as a presharpened microtip coupon. Our welding approach is versatile, as various metals could be used for sputtering, and allows similar flexibility as the GIS in principle.

Understanding the Degradation of a Model Si Anode in a Li-Ion Battery at the Atomic Scale

To advance the understanding of the degradation of the liquid electrolyte and Si electrode, and their interface, we exploit the latest developments in cryo-atom probe tomography. We evidence Si anode corrosion from the decomposition of the Li salt before charge-discharge cycles even begin. Volume shrinkage during delithiation leads to the development of nanograins from recrystallization in regions left amorphous by the lithiation. The newly created grain boundaries facilitate pulverization of nanoscale Si fragments, and one is found floating in the electrolyte. P is segregated to these grain boundaries, which confirms the decomposition of the electrolyte. As structural defects are bound to assist the nucleation of Li-rich phases in subsequent lithiations and accelerate the electrolyte's decomposition, these insights into the developed nanoscale microstructure interacting with the electrolyte contribute to understanding the self-catalyzed/accelerated degradation Si anodes and can inform new battery designs unaffected by these life-limiting factors.

Methods of Preparing Nanoscale Vitreous Ice Needles for High-Resolution Cryogenic Characterization

New high-resolution imaging methods for biological samples such as atom probe tomography (APT), facilitated by the invention of laser-pulsed atom probes and cryo-transfer procedures, have recently emerged. However, ensuring the vitreous state of the fabricated aqueous needle-shaped APT samples remains a challenge despite it being crucial for characterizing biomolecules such as proteins and cellular architectures in their near-native state. Our work investigated three potential approaches: (1) open microcapillary (OMC) method, (2) high-pressure freezing method (HPF), and (3) graphene encapsulation method. Diffraction patterns of the needle specimens acquired by cryo-TEM have demonstrated the vitreous state of the ice needles, although limited to the tip regions, has been achieved with the three proposed approaches. With the capability to prepare vitreous ice needles from hydrated samples of up to ∼200 μm thickness (HPF), combined use of the three approaches opens new avenues for future near-atomic imaging of biological cells in their near-native state.

Understanding the Underlying Field Evaporation Mechanism of Pure Water Tips in High Electrical Fields

We investigated the field evaporation process of frozen water in atom probe tomography (APT) by density functional simulations. In previous experiments, a strong tailing effect was observed for peaks caused by the molecular structure (H₂O)_nH⁺, in contrast to other peaks. In purely field-induced and thermally assisted evaporation simulations, we found that chains of protonated water molecules were pulled out of the dielectric surface by up to 6 Å, which are stable over a wide range of field strengths. Therefore, the resulting water clusters experience only part of the acceleration after evaporation compared to molecules evaporating directly from the surface and, thus, exhibit an energy deficit, which explains the tailing effect. Our simulations provide new insight into the complex evaporation behavior of water in high electrical fields and reveal possibilities for adapting the existing reconstruction algorithms.

Atomic-scale 3D imaging of individual dopant atoms in an oxide semiconductor

The physical properties of semiconductors are controlled by chemical doping. In oxide semiconductors, small variations in the density of dopant atoms can completely change the local electric and magnetic responses caused by their strongly correlated electrons. In lightly doped systems, however, such variations are difficult to determine as quantitative 3D imaging of individual dopant atoms is a major challenge. We apply atom probe tomography to resolve the atomic sites that donors occupy in the small band gap semiconductor Er(Mn,Ti)O3 with a nominal Ti concentration of 0.04 at. %, map their 3D lattice positions, and quantify spatial variations. Our work enables atomic-level 3D studies of structure-property relations in lightly doped complex oxides, which is crucial to understand and control emergent dopant-driven quantum phenomena.

Hydrogen and deuterium charging of lifted-out specimens for atom probe tomography

Hydrogen embrittlement can cause a dramatic deterioration of the mechanical properties of high-strength metallic materials. Despite decades of experimental and modelling studies, the exact underlying mechanisms behind hydrogen embrittlement remain elusive. To unlock understanding of the mechanism and thereby help mitigate the influence of hydrogen and the associated embrittlement, it is essential to examine the interactions of hydrogen with structural defects such as grain boundaries, dislocations and stacking faults. Atom probe tomography (APT) can, in principle, analyse hydrogen located specifically at such microstructural features but faces strong challenges when it comes to charging specimens with hydrogen or deuterium. Here, we describe three different workflows enabling hydrogen/deuterium charging of site-specific APT specimens: namely cathodic, plasma and gas charging. All the experiments in the current study have been performed on a model twinning induced plasticity steel alloy. We discuss in detail the caveats of the different approaches in order to help future research efforts and facilitate further studies of hydrogen in metals. Our study demonstrates successful cathodic and gas charging, with the latter being more promising for the analysis of the high-strength steels at the core of our work.

Hydrogen and deuterium charging of lifted-out specimens for atom probe tomography

Hydrogen embrittlement can cause a dramatic deterioration of the mechanical properties of high-strength metallic materials. Despite decades of experimental and modelling studies, the exact underlying mechanisms behind hydrogen embrittlement remain elusive. To unlock understanding of the mechanism and thereby help mitigate the influence of hydrogen and the associated embrittlement, it is essential to examine the interactions of hydrogen with structural defects such as grain boundaries, dislocations and stacking faults. Atom probe tomography (APT) can, in principle, analyse hydrogen located specifically at such microstructural features but faces strong challenges when it comes to charging specimens with hydrogen or deuterium. Here, we describe three different workflows enabling hydrogen/deuterium charging of site-specific APT specimens: namely cathodic, plasma and gas charging. All the experiments in the current study have been performed on a model twinning induced plasticity steel alloy. We discuss in detail the caveats of the different approaches in order to help future research efforts and facilitate further studies of hydrogen in metals. Our study demonstrates successful cathodic and gas charging, with the latter being more promising for the analysis of the high-strength steels at the core of our work.

Status and Direction of Atom Probe Analysis of Frozen Liquids

Imaging of liquids and cryogenic biological materials by electron microscopy has been recently enabled by innovative approaches for specimen preparation and the fast development of optimized instruments for cryo-enabled electron microscopy (cryo-EM). Yet, cryo-EM typically lacks advanced analytical capabilities, in particular for light elements. With the development of protocols for frozen wet specimen preparation, atom probe tomography (APT) could advantageously complement insights gained by cryo-EM. Here, we report on different approaches that have been recently proposed to enable the analysis of relatively large volumes of frozen liquids from either a flat substrate or the fractured surface of a wire. Both allowed for analyzing water ice layers which are several micrometers thick consisting of pure water, pure heavy water, and aqueous solutions. We discuss the merits of both approaches and prospects for further developments in this area. Preliminary results raise numerous questions, in part concerning the physics underpinning field evaporation. We discuss these aspects and lay out some of the challenges regarding the APT analysis of frozen liquids.

Design nanoporous metal thin films via solid state interfacial dealloying

Thin-film solid-state interfacial dealloying (thin-film SSID) is an emerging technique to design nanoarchitecture thin films. The resulting controllable 3D bicontinuous nanostructure is promising for a range of applications including catalysis, sensing, and energy storage. Using a multiscale microscopy approach, we combine X-ray and electron nano-tomography to demonstrate that besides dense bicontinuous nanocomposites, thin-film SSID can create a very fine (5-15 nm) nanoporous structure. Not only is such a fine feature among one of the finest fabrications by metal-agent dealloying, but a multilayer thin-film design enables creating nanoporous films on a wider range of substrates for functional applications. Through multimodal synchrotron diffraction and spectroscopy analysis with which the materials' chemical and structural evolution in this novel approach is characterized in details, we further deduce that the contribution of change in entropy should be considered to explain the phase evolution in metal-agent dealloying, in addition to the commonly used enthalpy term in prior studies. The discussion is an important step leading towards better explaining the underlying design principles for controllable 3D nanoarchitecture, as well as exploring a wider range of elemental and substrate selections for new applications.

Atom Probe Study of 1-Octadecanethiol Self-Assembled Monolayers on Platinum (111) and (200) Surfaces

Atom probe tomography measurements of self-assembled monolayers of 1-octadecanethiol on platinum tips were performed and their fragmentation behavior under the influence of different laser powers was investigated. The carbon backbone evaporates in the form of small hydrocarbon fragments consisting of one to four carbon atoms, while sulfur evaporates exclusively as single ions. The carbon molecules evaporate at very low fields of 5.9 V/nm, while S requires a considerably higher evaporation field of 23.4 V/nm. With increasing laser power, a weak, but noticeable trend toward larger fragment sizes is observed. No hydrocarbon fragments containing S are detected, indicating that a strong S–Pt bond has formed. The observed surface coverage of S fits well with literature values and is higher for (111)-oriented samples than for (200).

Atom Probe Tomography of a Cu-Doped TiNiSn Thermoelectric Material: Nanoscale Structure and Optimization of Analysis Conditions

Cu-doping and crystallographic site occupations within the half-Heusler (HH) TiNiSn, a promising thermoelectric material, have been examined by atom probe tomography. In particular, this investigation aims to better understand the influence of atom probe analysis conditions on the measured chemical composition. Under a voltage-pulsing mode, atomic planes are clearly resolved and suggest an arrangement of elements in-line with the expected HH (F-43m space group) crystal structure. The Cu dopant is also distributed uniformly throughout the bulk material. For operation under laser-pulsed modes, the returned composition is highly dependent on the selected laser energy, with high energies resulting in the measurement of excessively high absolute Ti counts at the expense of Sn and in particular Ni. High laser energies also appear to be correlated with the detection of a high fraction of partial hits, indicating nonideal evaporation behavior. The possible mechanisms for these trends are discussed, along with suggestions for optimal analysis conditions for these and similar thermoelectric materials.

Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy

Atom probe tomography, and related methods, probe the composition and the three-dimensional architecture of materials. The software tools which microscopists use, and how these tools are connected into workflows, make a substantial contribution to the accuracy and precision of such material characterization experiments. Typically, we adapt methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. We also realize that improving on research data management is a challenge when it comes to align with the FAIR data stewardship principles. Faced with this global challenge, we are convinced it is useful to join forces. Here, we report the results and challenges with an inter-laboratory call for developing test cases for several types of atom probe microscopy software tools. The results support why defining detailed recipes of software workflows and sharing these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to substantiated results.

3D sub-nanometer analysis of glucose in an aqueous solution by cryo-atom probe tomography

Atom Probe Tomography (APT) is currently a well-established technique to analyse the composition of solid materials including metals, semiconductors and ceramics with up to near-atomic resolution. Using an aqueous glucose solution, we now extended the technique to frozen solutions. While the mass signals of the common glucose fragments C_xH_y and C_xO_yH_z overlap with (H₂O)_nH from water, we achieved stoichiometrically correct values via signal deconvolution. Density functional theory (DFT) calculations were performed to investigate the stability of the detected pyranose fragments. This paper demonstrates APT’s capabilities to achieve sub-nanometre resolution in tracing whole glucose molecules in a frozen solution by using cryogenic workflows. We use a solution of defined concentration to investigate the chemical resolution capabilities as a step toward the measurement of biological molecules. Due to the evaporation of nearly intact glucose molecules, their position within the measured 3D volume of the solution can be determined with sub-nanometre resolution. Our analyses take analytical techniques to a new level, since chemical characterization methods for cryogenically-frozen solutions or biological materials are limited.

Atom probe tomography

Atom probe tomography (APT) provides three-dimensional compositional mapping with sub-nanometre resolution. The sensitivity of APT is in the range of parts per million for all elements, including light elements such as hydrogen, carbon or lithium, enabling unique insights into the composition of performance-enhancing or lifetime-limiting microstructural features and making APT ideally suited to complement electron-based or X-ray-based microscopies and spectroscopies. Here, we provide an introductory overview of APT ranging from its inception as an evolution of field ion microscopy to the most recent developments in specimen preparation, including for nanomaterials. We touch on data reconstruction, analysis and various applications, including in the geosciences and the burgeoning biological sciences. We review the underpinnings of APT performance and discuss both strengths and limitations of APT, including how the community can improve on current shortcomings. Finally, we look forwards to true atomic-scale tomography with the ability to measure the isotopic identity and spatial coordinates of every atom in an ever wider range of materials through new specimen preparation routes, novel laser pulsing and detector technologies, and full interoperability with complementary microscopy techniques.