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DOE OSTI2025

Etch Products of Copper Atomic Layer Etching by Oxidation and Formic Acid Vapor

Atomic layer etching (ALE) of metals offers a path to greater control of selectivity, etch rate, and etch profile. However, tailoring a process to meet these demands requires an understanding of the volatile etch product, which is challenging to detect due to low product concentrations and the paramagnetism of many metalorganic products. Here, in this work, several complementary analysis techniques were used to determine the volatile etch product and residual surface species of a Cu ALE process based on plasma oxidation and formic acid vapor etching of the oxidized layer. It was shown that the volatile product was copper formate with a Cu 2+ paramagnetic center, in concordance with prior density functional theory (DFT) calculations. While copper formate tetrahydrate was formed, it was determined that the tetrahydrate product was confined to the surface, with anhydrous copper formate being the volatile etch product.

Smith, Taylor G. [Univ. of California, Los Angeles↗

DOE OSTI2026

Surface Segregation of Liquid Metal Plasma-Facing Component Alloys: A ReaxFF Investigation

Engineering liquid metal alloys offers a transformative pathway for plasma-facing components by enabling chemically tailored surfaces that can simultaneously optimize plasma-material interactions, reduce divertor heat flux, and enhance core plasma confinement, thereby advancing the commercial viability of nuclear fusion power plants. This study, employing an atomistic simulation approach, provides direct evidence that incorporating nonmetal surface-active agents (such as O and H, or their combination) enables strong surface segregation. This capability makes tin−aluminum (Sn−Al) and tin−lithium (Sn−Li) alloys, with suitable compositions, good candidates for PFC applications. Specifically, the presence of low-Z solutes (Li, Al) leads to preferential surface enrichment, which imparts low-Z sputtering characteristics, while the Sn solvent maintains thermophysical stability. To systematically examine this behavior, we developed a ReaxFF force field spanning the full Sn/Al/Li/O/H chemistry, validated it against formation energies and elastic constants, and applied it in reactive molecular dynamics simulations at fusion-relevant temperatures. We also introduced an overlapbased segregation index that captures interfacial compositional separation directly from atomistic density distributions. Here, this metric reveals a clear hierarchy of segregation regimes and provides a unified view across all systems studied. Together, these findings establish a mechanistic link between nonmetal chemistry and interfacial structure, providing a predictive framework for designing self-adaptive, low-sputtering liquid metal alloys for fusion applications.

Alloys↗

DOE OSTI2019

Structure and Thermodynamic Stability of Zeolitic Imidazolate Framework Surfaces

Extensive efforts over the last several decades have focused on the possibility of “crystal engineering” metal–organic framework (MOF) materials with bulk properties tailored toward specific applications. However, beyond their bulk structure, MOF interfaces and surfaces can also play an important role in governing the materials properties relevant to many applications, including both interfacial mass and/or charge transport. We presently examine the diversity of stable surface structures/terminations of zeolitic imidazolate frameworks (ZIFs), a subclass of MOFs, under a variety of conditions that are characteristic of either gas-phase, “post-synthetic” conditions (relevant to many MOF applications) or solution-phase conditions (typical of those used during MOF synthesis). We construct surface phase diagrams to predict the most stable ZIF surface terminations as a function of external parameters (including temperature, adsorbate pressures, and pH), making explicit comparison against prior experimental observations, when possible. Overall, we find that the resulting phase diagrams can be used to explain the results of prior experimental studies of ZIF terminations across a variety of conditions and provide important insights into the factors that govern the structure of ZIF interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Spatially Offset Femtosecond Stimulated Raman Spectroscopy: Observing Exciton Transport through a Vibrational Lens

To design better molecular electronic devices, we need a strong understanding of how charges or excitons propagate, as many efficiency losses arise during transport. Exciton transport has been difficult to study because excitons tend to be short-lived, have short diffusion lengths, and can easily recombine. Here, we debut spatially offset femtosecond stimulated Raman spectroscopy (SO-FSRS), a three-pulse ultrafast microscopy technique. By offsetting the photoexcitation beam, we can monitor Raman spectral changes as a function of both time and position. We used SO-FSRS on 6,13-bis(triisopropylsilylethynyl) pentacene, a well-studied organic semiconductor used in photovoltaics and field-effect transistors. Furthermore, we demonstrated that the fast exciton and free charge carrier transport axes are identical and observed that exciton transport is less anisotropic by a factor of ~3. SO-FSRS is the first technique that directly tracks molecular structural evolution during exciton transport, which can provide roadmaps for tailor-making molecules for specific electronic devices.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Ion Mobility Spectrometry Characterization of the Intermediate Hydrogen-Containing Gold Cluster Au7(PPh3)7H52+

We employ ion mobility spectrometry and density functional theory to determine the structure of Au7(PPh3)7H52+ (PPh3 = triphenylphosphine) which was recently identified by high mass resolution mass spectrometry. Experimental ion-neutral collision cross sections represent the momentum transfer between the ionic clusters and gas molecules averaged over the relative thermal velocities of the colliding pair, thereby providing structural insights. Theoretical calculations indicate the geometry of Au7(PPh3)7H52+ is similar to Au7(PPh3)7+, with three hydrogen atoms bridging two gold atoms and two hydrogen atoms forming single Au–H bonds. Collision induced dissociation products observed during IMS experiments reveal that smaller hydrogen containing clusters may be produced through fragmentation of Au7(PPh3)7H52+. Our findings indicate that hydrogen containing species like Au7(PPh3)7H52+ act as intermediates in the formation of larger phosphine ligated gold clusters. These results advance the understanding and ability to control the mechanisms of size selective cluster formation which is necessary for scalable synthesis of clusters with tailored properties. This work was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. M.A.H. acknowledges support from the DOE Science Undergraduate Laboratory Internship (SULI) program. H.H. acknowledges support from the DOE Office of Workforce Development for Teachers and Scientist (WDTS) under the Visiting Faculty Program (VFP). The efforts of K.A.M. and B.H.C. were supported by the Defense Threat Reduction Agency (Grant No. HDTRA1-14-1-0023). The research was performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE under Contract DE-AC05-76RL01830.

Ligare, Marshall R.↗

DOE OSTI2022

Methyl-Driven Overhauser Dynamic Nuclear Polarization

The Overhauser effect is unique among DNP mechanisms in that it requires the modulation of the electron-nuclear hyperfine interactions. While it dominates DNP in liquids and metals, where unpaired electrons are highly mobile, Overhauser DNP is possible in insulating solids if rapid structural modulations are linked to a modulation in hyperfine coupling. In this study, we report that Overhauser DNP can be triggered by the strategic addition of a methyl group, demonstrated here in a Blatter’s radical. The rotation of the methyl group leads to a modulation of the hyperfine coupling to its protons, which in turn facilitates electron-nuclear cross-relaxation. Removal of the methyl protons, through deuteration, quenches the process, as does the reduction of the hyperfine coupling strength. This result suggests the possibility for the design of tailor-made Overhauser DNP polarizing agents for high-field MAS-DNP.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Determining Key Factors for the Open-Loop Control of Molecular Fragmentation Using Shaped Strong Fields

Pulse shaping has long been employed for tailoring femtosecond laser pulses to study and control the fragmentation of polyatomic molecules. In many cases, a physical explanation connecting the properties of the field to the observed control is difficult to ascertain. We utilized 80 bit binary spectral phase functions to parametrize and map the search space, gaining insight into which pulse parameters most impact the ion yield and fragmentation pattern for the relatively large triethylamine [N(C 2 H 5 ) 3 ] molecule. Pulse structures used to control the m/z 86 branching ratio beyond a simple intensity dependence are identified and compared to pump–probe results. All of these findings are explained in terms of control via a dissociative Rydberg state in the neutral molecule. This methodology may be used to discover new control mechanisms and shed light onto which pulse parameters most influence the interaction between strong field lasers and matter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Anode Potential Evolution During Zinc Metal Plating and Stripping in Dual-Solvent Battery Electrolytes

In the field of battery electrolyte research, the importance of the working cation solvation environment has become increasingly more apparent. To optimize bulk properties and, especially, interfacial reactions, multisolvent electrolytes (electrolytes containing two different solvents) have become more prevalent in battery research and development. In this work, we elucidate the relationship between cation solvation and interfacial electrochemistry, demonstrating that preferential solvation of Zn 2+ by a strong coordinating solvent such as 2-methoxyethylamine or ethylenediamine as opposed to a weaker solvent such as 3-methylsulfolane or acetonitrile leads to dynamic evolution in the interfacial energetics during Zn plating and stripping due to local changes in solvent composition and coordination. In some instances, interfacial solvation evolution can shift the reversible potential of Zn plating by as much as 1 V under relatively mild rate conditions. Through these investigations, we establish the generality of this phenomenon, highlight its importance as a consideration in dual-solvent battery electrolytes, and provide direction for tailoring electrochemistry through solvent design.

Hahn, Nathan T.↗

DOE OSTI2025

Accurate and Efficient Prediction of p K w in Aqueous Electrolytes Using Local Electrostatic Potentials

The K w =10 -pK w in aqueous electrolytes exhibit significant variations as a function of ion concentration. This behavior is not well-described by the Pitzer model, particularly at high concentrations. Here, we provide a molecular interpretation of the concentration dependent trends in p K w and develop a new method that accurately predicts the dissociation constant based upon the local electrostatic potential of the water oxygen that is determined by its nearest neighbors. The method is computationally efficient, relying only upon sampling of the local configurations (via molecular dynamics) and a small set of experimentally measured p K w . It is extensible to a range of salt compositions and the molecular understanding of the local potentials provides new routes toward the development of electrolytes with tailored physicochemical properties like p K w .

anions↗

DOE OSTI2026

Transition Metal Dichalcogenide MoS 2 : Oxygen and Fluorine Functionalization for Selective Plasma Processing

Low-temperature plasma processing is a promising technique for tailoring transition metal dichalcogenides (TMDs). For chalcogen substitution processing, a key challenge is to identify the ion energy window that enables selective chalcogen removal while preserving the metal lattice. Using ab initio molecular dynamics (AIMD), we demonstrate that oxygen and fluorine functionalization widen the processing window by significantly lowering the sulfur sputtering energy threshold (E sputt,S ) of MoS 2 from ∼30 to ∼10 eV via formation of sputtering products such as SO 2 and SF n . Additionally, we show that experimentally relevant cryogenic temperatures strongly affect E sputt,S (T). The dependence is confirmed via AIMD and also predicted by a mechanistic parameter-free theory, suggesting that E sputt (T) generalizes to other TMDs, functionalizations, and surface impact conditions. Our results highlight oxygen/fluorine functionalization, ionic impact angle, and material temperature to be key control parameters for selective, damage-controlled chalcogen removal in TMD processing.

Polyachenko, Yury [Princeton Plasma Physics Labora↗

DOE OSTI2026

Pore-Selective Fullerene Loading in a Porphyrin-Based Metal–Organic Framework Controls Photoinduced Charge-Transfer Dynamics

Building porous donor−acceptor networks based on host−guest interactions in metal organic frameworks (MOFs) provides unique opportunities for tuning charge separation in highly tailorable materials. Here we focus on installing electron-rich porphyrins and electron-deficient fullerene derivatives in the PCN-222 MOF using a solvent assisted ligand insertion (SALI) method. The fullerene is primarily bound in the large pore, where it is subject to distinct dielectric environments through dimethylformamide (DMF) and 1,4-dioxane solvent exchange. Following photoexcitation, sub-picosecond charge transfer involving initial exciplex population is observed, with different charge recombination pathways and lifetimes depending on solvent polarity through modulation of charge-transfer state energies. While the 1,4-dioxane environment yields charge recombination within 1 ns via local fullerene and porphyrin triplet state population, DMF results in charge recombination directly to the ground state on much longer time scales, including some lifetime components in the microsecond range. Fullerene loading influences these kinetics, and the potential for charge delocalization due to fullerene aggregation within the pores is evaluated by using molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

pmartR 2.0 : A Quality Control, Visualization, and Statistics Pipeline for Multiple Omics Datatypes

The pmartR (https://github.com/pmartR/pmartR) package was designed for the quality control (QC) and analysis of mass spectrometry (MS) data, tailored to specific characteristics of proteomic (isobaric or labelled), metabolomic, and lipidomic datasets. Since its initial release, the tool has been expanded to address the needs of its growing userbase and now includes QC and statistics for nuclear magnetic resonance (NMR) metabolomic data, and leverages the DESeq2, edgeR, and limma-voom R packages for some transcriptomic data analyses. These improvements have made progress towards a unified omics processing pipeline for ease of reporting and streamlined statistical purposes. The package’s statistics and visualization capabilities have also been expanded by adding support for paired data and by integrating pmartR with the trelliscopejs R package for the quick creation of trellis displays (https://github.com/hafen/trelliscopejs). Here, we present relevant examples of each of these enhancements to pmartR and highlight how each new feature benefits the omics community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Aggregation Methods for Quantifying PTM and Structural Changes in Bottom-Up Proteomics

Bottom-up proteomic workflows rely on sequential preprocessing steps, commonly including peptide-to-protein aggregation (“roll-up”), to enhance data reliability and interpretability. While roll-up is effective for protein-centered analyses, it may be suboptimal for applications focused on post-translational modifications (PTMs) or protein structural changes, such as limited proteolysis–mass spectrometry (LiP-MS). Here, we investigate how different roll-up strategies influence site-level quantification in PTM differential analysis. Moreover, we introduce a novel site-centric roll-up approach tailored for LiP-MS, which quantifies proteolytic fragments rather than solely tryptic peptides. We benchmark these methods through simulation studies, comparing their sensitivity and specificity in detecting structural and PTM-driven changes. We found that the median and mean roll-up methods outperform the sum method in both PTM and LiP proteomics, and site-level quantification in LiP outperforms peptide-level quantification. Our findings offer the first systematic, data-driven guidance for selecting roll-up techniques in site-level proteomic analyses, with implications for both PTM-focused and structural proteomics studies.

aggregation↗

DOE OSTI2026

OmicsMLMentor: A Web Application for Guided Machine Learning Analysis of Omics Data

Expression-based omics technologies (e.g. proteomics, metabolomics, transcriptomics, etc.) increasingly rely on supervised and unsupervised machine learning (ML) models to find key biomolecules distinguishing conditions, identify natural groupings in biological data, or generate predictions for outcomes of interest. Fitting ML models to omics data presents several challenges, including handling missing data, selecting a normalization method, choosing a valid model, and optimizing hyperparameters, all requiring statistical programming skills to address these challenges. Thus, the open-source web application SLOPE was designed to lower the barrier to ML modeling for omics data. SLOPE supports the fitting of 15 ML models (10 supervised and 5 unsupervised) tailored to omics datasets, such as proteomics, metabolomics, lipidomics, and transcriptomics. SLOPE offers several omics-specific features, including methods for handling missingness (imputation, conversion, removal), normalization tests, ranking of models based on the structure of a user’s data and user input, and optimal hyperparameter selections using cross-validation splits. By streamlining ML workflows for omics analysis, SLOPE address critical gaps in existing online web tools, facilitating a broader adoption of these models for omics research. Here, SLOPE is applied to data from a lignin exposure study to highlight the workflow for fitting both supervised and unsupervised models to data.

lipidomics↗

DOE OSTI2020

Mapping the Interfacial Chemistry and Structure of Partially Fluorinated Bottlebrush Polymers and Their Linear Analogues

Polymer interfaces are key to a range of applications including membranes for chemical separations, hydrophobic coatings, and passivating layers for antifouling. While important, challenges remain in probing the interfacial monolayer where the molecular ordering and orientation can change depending on the chemical makeup or processing conditions. In this work, we leverage surface specific vibrational sum frequency generation (SFG) and the associated dependence on molecular symmetry to elucidate the ordering and orientations of key functional groups for poly(2,2,2-trifluoroethyl methacrylate) bottlebrush polymers and their linear polymer analogues. These measurements were framed by atomistic molecular dynamic simulations to provide a complementary physical picture of the gas–polymer interface. Simulations and SFG measurements show that methacrylate backbones are buried beneath a layer of trifluoroethyl containing side groups that result in structurally similar interfaces regardless of the polymer molecular weight or architecture. The average orientational angles of the trifluoroethyl containing side groups differ depending on polymer linear and bottlebrush architectures, suggesting that the surface groups can reorient via available rotational degrees of freedom. Results show that the surfaces of the bottlebrush and linear polymer samples do not strongly depend on molecular weight or architecture. As such, one cannot rely on increasing the molecular weight or altering the architecture to tune surface properties. This insight into the polymer interfacial structure is expected to advance the design of new material interfaces with tailored chemical/functional properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Functionalized Polymersomes from a Polyisoprene-Activated Polyacrylamide Precursor

Self-assembled polymer nanoparticles have tremendous potential in biomedical and environmental applications. For all applications, tailored polymer chemistries are critical. In this study, we demonstrate a precursor approach in which an activated, organic solvent-soluble block polymer precursor is modified through mild postpolymerization modifications to access new polymer structures. We synthesized and characterized poly(isoprene)-block-poly(di-Boc acrylamide) diblock polymers. This activated-acrylamide-based polymer was then reacted with amines or reductants in the absence of catalysts to yield the hydrophilic blocks polyacrylamide, poly(hydroxypropylene), and poly(N-ethyl acrylamide). The resulting amphiphilic block polymers self-assembled in water to form polymersomes, as confirmed by cryo-electron microscopy and confocal microscopy. The approach also enables simple functionalization with specialized ligands, which we demonstrated by tagging polymers with an amino-fluorophore and imaging by confocal microscopy. Here, we expect that the methodologies established in this study will open doors to new and useful solution nanostructures with surface chemistries that can be optimized for various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Surface Zeta Potential of ALD-Grown Metal-Oxide Films

Membranes are among the most promising technologies for energy-efficient and highly selective separations, and the surface-charge property of membranes plays a critical role in their broad applications. Atomic layer deposition (ALD) can deposit materials uniformly and with high precision and controllability on arbitrarily complex and large substrates, which renders it a promising method to tune the electrostatics of water/solid interfaces. However, a systematic study of surface-charge properties of ALD-grown films in aqueous environments is still lacking. In this work, 17 ALD-grown metal-oxide films are synthesized, and a comprehensive study of their water stability, wetting properties, and surface-charge properties is provided. Furthermore, this work represents a resource guide for researchers and ultimately for materials and process engineers, seeking to tailor interfacial charge properties of membranes and other porous water treatment components.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Electrodeposition of Complex High Entropy Oxides via Water Droplet Formation and Conversion to Crystalline Alloy Nanoparticles

We report that a combination of electrodeposition and thermal reduction methods have been utilized for the synthesis of ligand-free FeNiCo alloy nanoparticles through a high-entropy oxide intermediate. These phases are of great interest to the electrocatalysis community, especially when formed by a sustainable chemistry method. This is successfully achieved by first forming a complex five element amorphous FeNiCoCrMn high-entropy oxide (HEO) phase via electrodeposition from a nanodroplet emulsion solution of the metal salt reactants. The amorphous oxide phase is then thermally treated and reduced at 570–600 °C to form the crystalline FeNiCo alloy with a separate CrMnO x cophase. The FeNiCo alloy is fully characterized by scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy elemental analysis and is identified as a face-centered cubic crystal with the lattice constant a = 3.52 Å. The unoptimized, ligand-free FeNiCo NPs activity toward the oxygen evolution reaction is evaluated in alkaline solution and found to have an ~185 mV more cathodic onset potential than the Pt metal. Beyond being able to synthesize highly crystalline, ligand-free FeNiCo nanoparticles, the demonstrated and relatively simple two-step process is ideal for the synthesis of tailor-made nanoparticles where the desired composition is not easily achieved with classical solution-based chemistries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗