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DOE OSTI2025

Design principles of spacer cations for suppressing phase segregation in 2D halide perovskites

Suppression of photoinduced halide segregation in mixed halide perovskites remains a significant challenge for their application as wide bandgap semiconductors in solar cells. In addition to stability issues, halide segregation leads to a loss in power conversion efficiency in solar cells and a shift in emission wavelength in light-emitting devices. However, employing low-dimensional halide perovskites, such as two-dimensional (2D) or quasi-2D structures, offers a strategy to mitigate this segregation. Here, we have systematically studied how the molecular structure and binding configuration of spacer cations, ranging from linear alkyl chains to aromatic structures, affect photoinduced halide segregation across both Ruddlesden–Popper (RP) and Dion–Jacobson (DJ) frameworks in 2D mixed halide perovskites (Br : I = 50 : 50). Aromatic spacer cations within the DJ perovskite configuration were found to suppress segregation most effectively. For example, the halide segregation rate in a 2D mixed halide perovskite film with the DJ phase using the aromatic spacer cation 1,4-phenylenedimethanammonium (PDMA) was 9.3 × 10 −4 s −1 —an order of magnitude lower than that observed with linear 2D RP perovskites employing butylammonium (BA) as the spacer cation (6.1 × 10 −3 s −1 ). Spectroscopic studies detailing the influence of spacer cation selection in mixed halide perovskites for suppressing phase segregation are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Composition-Nanoarchitecture-Performance Analysis of High Energy Density Electrodeposited Silicon for Lithium-Ion Battery Anodes

Electrodeposition of silicon (Si) was previously demonstrated as a promising method for fabricating 3D-structured lithium-ion battery anodes. However, the relationship between the electrochemical performance and chemical composition of the relatively impure electrodeposited silicon is not well understood. Here, we report the electrodeposition of a Si-dominant active material (EDEP-Si) onto 3D-structured nickel (Ni) scaffolds and systematically compare the electrochemical properties, elemental composition, atomistic Si coordination, and molecular structure of EDEP-Si with high-purity amorphous Si grown via static chemical vapor deposition. Despite the considerable amount of carbon (9–11 at %) and oxygen (42–44 at %) present in EDEP-Si, the cycling stability and high reversible specific capacity are remarkably similar to those of CVD-Si on a silicon basis (~2400 mA h/g-Si after 100 cycles). The primary difference is that EDEP-Si exhibits reduced cycling efficiency over the first 10–20 cycles. Reactions between carbon and, more importantly, oxygen in EDEP-Si with lithium are likely responsible for the reduced early cycle performance and lower capacity of the total deposit. Finally, our observations suggest ultrapure Si is not necessary for high electrochemical access to reversible charge storage, although limiting the presence of incorporated impurity species would improve energy density and first cycle efficiency.

25 ENERGY STORAGE↗

DOE OSTI2025

Generalizable, fast, and accurate DeepQSPR with fastprop

Abstract Quantitative Structure–Property Relationship studies (QSPR), often referred to interchangeably as QSAR, seek to establish a mapping between molecular structure and an arbitrary target property. Historically this was done on a target-by-target basis with new descriptors being devised to specifically map to a given target. Today software packages exist that calculate thousands of these descriptors, enabling general modeling typically with classical and machine learning methods. Also present today are learned representation methods in which deep learning models generate a target-specific representation during training. The former requires less training data and offers improved speed and interpretability while the latter offers excellent generality, while the intersection of the two remains under-explored. This paper introduces , a software package and general Deep-QSPR framework that combines a cogent set of molecular descriptors with deep learning to achieve state-of-the-art performance on datasets ranging from tens to tens of thousands of molecules. provides both a user-friendly Command Line Interface and highly interoperable set of Python modules for the training and deployment of feedforward neural networks for property prediction. This approach yields improvements in speed and interpretability over existing methods while statistically equaling or exceeding their performance across most of the tested benchmarks. is designed with Research Software Engineering best practices and is free and open source, hosted at github.com/jacksonburns/fastprop.

Burns, Jackson W. (ORCID:0000000206579426)↗

DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗

DOE OSTI2024

Small‐Molecule Mixed Ionic‐Electronic Conductors for Efficient N‐Type Electrochemical Transistors: Structure‐Function Correlations

Abstract The fundamental challenge in electron‐transporting organic mixed ionic‐electronic conductors (OMIECs) is simultaneous optimization of electron and ion transport. Beginning from Y6‐type/U‐shaped non‐fullerene solar cell acceptors, we systematically synthesize and characterize molecular structures that address the aforementioned challenge, progressively introducing increasing numbers of oligoethyleneglycol (OEG; g) sidechains from 1 g to 3 g, affording OMIECs 1gY, 2gY, and 3gY, respectively. The crystal structure of 1gY preserves key structural features of the Y n series: a U‐shaped/planar core, close π–π molecular stacking, and interlocked acceptor groups. Versus inactive Y6 and Y11, all of the new glycolated compounds exhibit mixed ion‐electron transport in both conventional organic electrochemical transistor (cOECT) and vertical OECT (vOECT) architectures. Notably, 3gY with the highest OEG density achieves a high transconductance of 16.5 mS, an on/off current ratio of ~10 6 , and a turn‐on/off response time of 94.7/5.7 ms in vOECTs. Systematic optoelectronic, electrochemical, architectural, and crystallographic analysis explains the superior 3gY‐based OECT performance in terms of denser n gY OEG content, increased crystallite dimensions with decreased long‐range crystalline order, and enhanced film hydrophilicity which facilitates ion transport and efficient redox processes. Finally, we demonstrate an efficient small‐molecule‐based complementary inverter using 3gY vOECTs, showcasing the bioelectronic applicability of these new small‐molecule OMIECs.

Cho, Yongjoon↗

DOE OSTI2024

Small‐Molecule Mixed Ionic‐Electronic Conductors for Efficient N‐Type Electrochemical Transistors: Structure‐Function Correlations

Cho, Yongjoon↗

DOE OSTI2025

Impact of Halogen Groups on the Properties of PEA–Based 2D Pb–Sn Halide Perovskites

Tuning broad emission in 2D Pb–Sn halide perovskites (HPs) is essential for advancing optoelectronic applications, particularly for color-tunable and white-light-emitting devices. This broad emission is linked to structural factors, such as defects and phase segregation of the Pb component within the Pb–Sn system, which are strongly influenced by the molecular structure and chemical properties of spacer cations. Atomic tuning of the spacers via halogenation opens up a new way to fine-tune the molecular properties, enabling further augmentations of HP functionalities. Nevertheless, the distinct broad emission's sensitivity to spacer chemistry remains underexplored. Here, halogenation's influence is systematically investigated on 2D HP emission characteristics using a high-throughput workflow. These findings reveal that the F-containing phenethylammonium (4F-PEA) spacer narrows the broadband PL, whereas Cl broadens it. Through a correlative study, it is found that 4F-PEA reduces not only the local phase segregation but also the defect levels and microstrains in 2D HPs. This is likely attributed to the manifestation of less lattice distortion via stronger surface coordination of the dipole-augmented 4F-PEA. Furthermore, these results highlight halogenation as a key factor in modulating phase segregation and defect density in 2D Pb–Sn HPs, offering a promising pathway to tune the emission for enhanced optoelectronic performance.

2D Pb-Sn halide perovskites↗

DOE OSTI2025

Paired Neural Network for Matching Experimental and Predicted Infrared Spectra

Here, we present a novel machine learning (ML)-based scoring technique for determining the similarity between experimental and predicted infrared (IR) spectra for identification purposes. IR spectroscopy is a powerful technique used to identify the molecular structure and composition of a sample by measuring the unique vibrational frequency pattern of the molecule’s functional groups. Molecular identifications are often made by comparing experimental and reference spectra. However, the limited number of reference spectra available in spectral libraries can confound the identification process. Alternative identification procedures rely on in silico techniques to simulate spectra for a wide range of molecules. However, scoring spectral similarity between an experimental query and computationally predicted reference remains a significant challenge. Our proposed ML-based scoring technique overcomes these barriers by accurately and efficiently determining spectral similarity.

Neural Network↗

DOE OSTI2025

Advancing molecular machine learning representations with stereoelectronics-infused molecular graphs

Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have used strings, fingerprints, global features and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a new approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects, enhancing expressivity and interpretability. Learning to predict the stereoelectronics-infused representation with a tailored double graph neural network workflow enables its application to any downstream molecular machine learning task without expensive quantum-chemical calculations. We show that the explicit addition of stereoelectronic information substantially improves the performance of message-passing two-dimensional machine learning models for molecular property prediction. We show that the learned representations trained on small molecules can accurately extrapolate to much larger molecular structures, yielding chemical insight into orbital interactions for previously intractable systems, such as entire proteins, opening new avenues of molecular design. Finally, we have developed a web application (simg.cheme.cmu.edu) where users can rapidly explore stereoelectronic information for their own molecular systems.

Boiko, Daniil A↗

DOE OSTI2025

Synthesis, structure, and stability of a novel 2 H -azirine under pressure

We have synthesized 2,3-diphenyl-2H-azirine, a strained unsaturated heterocyclic compound, and examined its high-pressure behavior to above 10 GPa using diamond anvil cell techniques. Single crystal X-ray diffraction at ambient conditions reveals that the crystal structure is hexagonal and consists of interesting helices surrounding voids in the structure. A continuous shift of the Raman and infrared vibrational spectra with increasing pressure is observed, indicating that the molecular structure is preserved to at least 8 GPa at room temperature. High-pressure synchrotron powder X-ray diffraction shows that the hexagonal structure persists, with a smooth compression of the a and c parameters to 10 GPa. The structural stability under pressure is attributed to the reduction in void size within the helical framework despite the inherent strain and reactivity of the molecule. The channels in the structure could encapsulate small molecules for gas or energy storage applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Structured for success: conjugated polymer binders with tailored composition and architecture for lithium-ion batteries

Conjugated polymer binders are replacing conventional binders in lithium-ion batteries. Herein, we examine how molecular engineering and hierarchical nanostructuring govern binder functionality and electrochemical performance. Lithium-ion batteries (LIBs) are the leading energy storage technology, yet enhancing their energy density and cycle life remains critical. Significant progress has been made in high-capacity anodes and high-voltage cathodes, but their performance is hindered by electrode degradation, where it is related to the behaviors of binders at the surface and interface. Conventional non-conductive binders like poly(vinylidene difluoride) (PVDF), combined with conductive additives, often fail to maintain electrical pathways under repeated volume changes. Alternatively, conjugated polymer binders have emerged as a superior alternative, simultaneously offering intrinsic conductivity, mechanical flexibility, and strong adhesion through π-conjugated backbones and functional groups. Their tunable molecular structure enables efficient electron/ion transport while mitigating electrode cracking. Additionally, the development of hierarchically ordered nanostructures in conjugated polymer binder can further enhance their electrochemical performance. This review examines the design principles of conjugated polymer binders, focusing on molecular engineering and nanostructural control to optimize their performance in high-loading electrodes, such as silicon-based anodes. By addressing key challenges in binder functionality, these advanced materials pave the way for next-generation high-energy-density LIBs.

Jin, Xiuyu↗

DOE OSTI2025

Advanced Modeling and Process-Materials Co-Optimization Strategies for Swing Adsorption Based Gas Separations

This project devised a computational framework for simultaneously co-optimizing pressure swing adsorption process designs along with the sorbent materials (specifically, metal-organic frameworks) to be employed in the associated packed bed columns. The materials optimization aspect involved search over a design space that can describe the material’s molecular structure, while the process optimization aspect considered various process degrees of freedom for steps arising in various cycle configurations. This framework was demonstrated on the separation of nitrogen and carbon dioxide, which arises ubiquitously in a multitude of post-combustion carbon capture and “blue” hydrogen production applications. Our results led to metal-organic framework molecular descriptor choices that are predicted to outperform standard structures used in practice, providing guidance for future metal-organic framework synthesis efforts.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2026

Experimental Quantification of Spin–Phonon Coupling in Molecular Qubits Using Inelastic Neutron Scattering

Electronic spin superposition states enable nanoscale sensing through their sensitivity to the local environment, yet their sensitivity to vibrational motion also limits their coherence times. In molecular spin systems, chemical tunability and atomicscale resolution are accompanied by a dense, thermally accessible phonon spectrum that introduces efficient spin relaxation pathways. Despite extensive theoretical work, there is little experimental consensus on which vibrational energies dominate spin relaxation or how molecular structure controls spin−phonon coupling (SPC). We present a fully experimental method to quantify SPC coefficients by combining temperature-dependent vibrational spectra from inelastic neutron scattering with spin relaxation rates measured by electron paramagnetic resonance. We apply this framework to two model S = 1/2 systems, copper(II) phthalocyanine (CuPc) and copper(II) octaethylporphyrin (CuOEP). Two distinct relaxation regimes emerge: below 40 K, weakly coupled lattice modes below 50 cm −1 dominate, whereas above 40 K, optical phonons above ∼185 cm −1 become thermally populated and drive relaxation with SPC coefficients nearly 3 orders of magnitude larger. Structural distortions in CuOEP that break planar symmetry soften the crystal lattice and enhance anharmonic scattering but also raise the energy of stretching modes at the molecular core where the spins reside. This redistributes vibrational energy toward the molecular periphery and out of plane, ultimately reducing SPC relative to CuPc and enabling room-temperature spin coherence in CuOEP. Although our method does not provide mode-specific SPC coefficients, it quantifies contributions from distinct spectral regions and establishes a broadly applicable, fully experimental link between crystal structure, lattice dynamics, and spin relaxation.

Lohaus, Stefan H. [California Institute of Technol↗

DOE OSTI2026

Tailoring Crosslinks through Time─A Paradigm for Tough Hydrogels

The multidisciplinary applications of hydrogels have motivated a thorough exploration of the relationship between their structural and mechanical properties, i.e., spatial structure–function relationships, with particular regard to strength and toughness. While this approach has driven fundamental advancements in the design of robust hydrogel structures, further complementary perspectives are needed to enable holistic, rational design schemes that integrate considerations such as fabrication and advanced functions like response and adaptation. To these ends, this review focuses on the dynamics of temporal-function relationships and their fundamental bases in order to highlight how the dynamic regulation of polymer interactions programs: 1) polymer assembly and material structure; 2) response to deformation and fracture behavior; 3) dynamic modulation of properties and structural remodeling/self-healing. Here, by exploring this intersection of hydrogel formation, function, and remodeling, this review seeks to shed light on the fundamental relationship between molecular structure, material assembly, and performance in order to connect the emerging area of bioinspired materials processing with tough hydrogel design, and further provides a lasting inspiration and impetus for future hydrogel development that enables valuable scientific and technological advancements.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Metalloproteins in an Era of Modern Crystallography and Why the Beamline Matters

The Structural Molecular Biology (SMB) macromolecular crystallography (MC) group at the Stanford Synchrotron Radiation Lightsource (SSRL) have developed state-of-the-art capabilities tailored for metalloenzyme structural analysis. Metalloproteins sit at the center of biology’s most audacious chemistry. From multi-electron redox catalysis to radical rearrangements and light-driven transformations, metal sites give proteins access to reaction landscapes that would otherwise be inaccessible under ambient conditions. Yet their study presents a fundamental paradox for MC studies: the very X-rays we use to reveal atomic structure can alter the electronic states we seek to understand. As the field moves beyond static snapshots toward mechanistic insight, success increasingly depends on our ability to maintain metal centers in their native state throughout the experiment. The SSRL SMB-MC beamlines integrate a suite of capabilities specifically designed to address these challenges. By combining in situ spectroscopic verification, intelligent dose management, controlled reaction initiation, optimized anomalous diffraction, and real-time crystallographic diffraction analysis, these tools enable researchers to interrogate metalloproteins with unprecedented rigor. This article explores how these complementary approaches are reshaping our ability to capture metalloprotein chemistry, and what this means for mechanistic studies at synchrotron beamlines.

Maggiolo, Ailiena O. [SLAC National Accelerator La↗

DOE OSTI2025

Chemically Enhanced Electrodialysis (CEED) for Recovery of Rare Earth Elements

Rare-earth elements are crucial for numerous technologically relevant industries including energy, electronics, and aerospace; however, both the supply and separation of rare earths are pressing challenges. The long-term goal of the collaborative project is to develop a novel approach to existing extraction behaviors. To achieve this goal, a class of electrodialysis membranes with novel ion-gating functionality will be developed and paired with a conventional electrodialysis strategy. The hypothesis of the work is that incorporating sequestrants of suitable structures at the surface of the electrodialysis membrane will enhance extraction efficiency for ions of interest. Our ability to prepare sequestrants of diverse conformations and to adapt their molecular structure for binding lanthanides renders the proposed technology a versatile method for selective ion separation. Our approach will enable an entirely new technological approach to the separation of valuable rare-earth elements.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Investigating Lignin Aggregation and Interactions with Solvents during γ-Valerolactone (GVL) Pretreatment: A Combined Small Angle Neutron Scattering and Molecular Simulations Study

The strong tendency of lignin to aggregate in solution, coupled with limited understanding of how its molecular structure governs this behavior, hinders its effective utilization in biorefineries. Here, in this study, we investigated the solution behavior of lignin extracted from poplar using γ-valerolactone/water (GVL/H2O, 9:1 wt/wt) through combined small-angle neutron scattering (SANS) and molecular dynamics (MD) simulations. Lignin samples obtained at 100 °C (L100) and 120 °C (L120) differed in β–O–4 content, hydroxyl distribution, and S/G ratio, enabling direct assessment of how molecular composition governs solvation and aggregation. SANS showed that L120 formed rigid and elongated cylindrical aggregates at 25 °C that transitioned to more flexible spheroidal structures by 50 °C and remained stable up to 80 °C, whereas L100 adopted globular aggregates that progressively collapsed with increasing temperature. MD simulations reinforced these observations by showing that S-rich (L120-like) oligomers had larger radii of gyration, stronger solvent coordination driven by methoxy groups, and fewer lignin–lignin contacts. In contrast, G-rich (L100-like) oligomers displayed persistent aggregation and lower solubility. Collectively, these results reveal that increased aromatic methoxylation enhances lignin–solvent interactions and suppresses self-association, whereas reduced methoxylation and higher β–O–4 content promote persistent aggregation into colloid-like structures with restricted solvent penetration into the aggregate interior.

biorefinery pretreatment↗

DOE OSTI2026

ENVnet provides a global molecular resource of dissolved organic matter

Dissolved organic matter (DOM) is an important component of Earth's carbon cycle and one of the planet's most chemically diverse pools, yet the molecular structures of its constituents remain largely unresolved. This limitation has hindered our ability to link DOM composition to microbial processes and ecosystem function. Here we present ENVnet, a global molecular repository built from tandem mass spectrometry data collected across 13 terrestrial and aquatic environment types, including 419 newly generated samples that expand publicly available DOM metabolomics data and cover previously underrepresented environments. By computationally deconvolving chimeric mass spectra, a longstanding challenge in environmental metabolomics, we recover high-quality fragmentation data for >22,000 distinct molecular features (defined by a specific precursor mass and fragmentation pattern). Using ENVnet, we uncover conserved and environment-specific molecular patterns in DOM composition and underlying biogeochemical processes. We also use molecular features encoded in ENVnet to train predictive models of DOM persistence, allowing molecular-level assessment of microbial turnover in independent systems.

54 ENVIRONMENTAL SCIENCES↗