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At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Sequence Design of Random Heteropolymers as Protein Mimics

Random heteropolymers (RHPs) have been computationally designed and experimentally shown to recapitulate protein-like phase behavior and function. However, unlike proteins, RHP sequences are only statistically defined and cannot be sequenced. Recent developments in reversible-deactivation radical polymerization allowed simulated polymer sequences based on the well-established Mayo–Lewis equation to more accurately reflect ground-truth sequences that are experimentally synthesized. This led to opportunities to perform bioinformatics-inspired analysis on simulated sequences to guide the design, synthesis, and interpretation of RHPs. We compared batches on the order of 10000 simulated RHP sequences that vary by synthetically controllable and measurable RHP characteristics such as chemical heterogeneity and average degree of polymerization. Our analysis spans across 3 levels: segments along a single chain, sequences within a batch, and batch-averaged statistics. We discuss simulator fidelity and highlight the importance of robust segment definition. Examples are presented that demonstrate the use of simulated sequence analysis for in-silico iterative design to mimic protein hydrophobic/hydrophilic segment distributions in RHPs and compare RHP and protein sequence segments to explain experimental results of RHPs that mimic protein function. To facilitate the community use of this workflow, the simulator and analysis modules have been made available through an open source toolkit, the RHPapp.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

First-Principles Statistical Mechanics Study of Magnetic Fluctuations and Order–Disorder in the Spinel LiNi 0.5 Mn 1.5 O 4 Cathode

While significant magnetic interactions exist in lithium transition metal oxides, commonly used as Li-ion cathodes, the interplay between magnetic couplings, disorder, and redox processes remains poorly understood. In this work, we focus on the high-voltage spinel LiNi 0.5 Mn 1.5 O 4 (LNMO) cathode as a model system on which to apply a computational framework that uses first principles-based statistical mechanics methods to predict the finite temperature magnetic properties of materials and provide insights into the complex interplay between magnetic and chemical degrees of freedom. Density functional theory calculations on multiple distinct Ni–Mn orderings within the LNMO system, including the ordered ground-state structure (space group P4332), reveal a preference for a ferrimagnetic arrangement of the Ni and Mn sublattices due to strong antiferromagnetic superexchange interactions between neighboring Mn 4+ and Ni 2+ ions and ferromagnetic Mn–Mn and Ni–Ni couplings, as revealed by magnetic cluster expansions. These results are consistent with qualitative predictions using the Goodenough-Kanamori-Anderson rules. Simulations of the finite temperature magnetic properties of LNMO are conducted using Metropolis Monte Carlo. We find that a “semiclassical” Monte Carlo sampling method based on the Heisenberg Hamiltonian accurately predicts experimental magnetic transition temperatures observed in magnetometry measurements. This study highlights the importance of a robust computational toolkit that accurately captures the complex chemomagnetic interactions and predicts finite temperature magnetic behavior to help analyze experimental magnetic and magnetic resonance spectroscopy data acquired ex situ and operando.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Structural Propensities in Cs2MBiX6 (M=Na, Ag; X=Cl, Br) Bismuth Halide Double Perovskites

A previously unreported low-temperature phase transition in the bismuth halide double perovskite Cs2AgBiCl6 is reported, thereby establishing trends in the structural ground state across Cs2NaBiCl6, Cs2AgBiCl6, and Cs2AgBiBr6. Using the combined toolkit of variable-temperature synchrotron X-ray and neutron powder diffraction, Raman spectroscopy, and density-functional theory–based electronic structure modeling, we demonstrate a cubic Fm¯3m → tetragonal I4/m transition upon cooling with distinct onset temperatures. Neutron powder diffraction refinements permit the unambiguously assignment of the low-temperature phase of Cs2NaBiCl6 to I4/m, correcting prior reports of an I4/mmm ground state. Cs2AgBiCl6 is also found to transforms to a structure crystallizing in the I4/m space group at low temperatures. Temperaturedependent Raman data and density-functional theory-based modeling capture the softening and freezing of out-of-phase octahedral-tilt modes and quantify relative instabilities. Solid-state nuclear magnetic resonance spectroscopy at room temperature completes the characterization and helps underpin the subtle differences in covalency across the compounds. Trends in the phase transition temperature Ts and tilt magnitudes emerge from coupled effects of halide identity, M(I)–site bonding character, and a mismatch between interatomic distances. These results establish the structure– dynamics–bonding framework for tuning tilt-driven instabilities in halide double perovskites.

Tian, Haowen↗
DOE OSTI2017

Order–Disorder Transitions and Superionic Conductivity in the Sodium nido -Undeca(carba)borates

The salt compounds NaB 11 H 14 , Na-7-CB10H13, Li-7-CB 10 H 13 , Na-7,8-C 2 B 9 H 12 , and Na-7,9-C 2 B 9 H 12 all contain geometrically similar, monocharged, nido-undeca(carba)borate anions (i.e., truncated icosohedral-shaped clusters constructed of only 11 instead of 12 {B-H} + {C-H} vertices and an additional number of compensating bridging and/or terminal H atoms). We used first-principles calculations, X-ray powder diffraction, differential scanning calorimetry, neutron vibrational spectroscopy, neutron elastic-scattering fixed-window scans, quasielastic neutron scattering, and electrochemical impedance measurements to investigate their structures, bonding potentials, phase-transition behaviors, anion orientational mobilities, and ionic conductivities compared to those of their closo-poly(carba)borate cousins. All exhibited order-disorder phase transitions somewhere between room temperature and 375 K. All disordered phases appear to possess highly reorientationally mobile anions (> ~10 10 jumps s -1 above 300 K) and cation-vacancy-rich, close-packed or body-center-cubic-packed structures [like previously investigated closo-poly(carba)borates]. Moreover, all disordered phases display superionic conductivities but with generally somewhat lower values compared to those for the related sodium and lithium salts with similar monocharged 1-CB 9 H 10 - and CB 11 H 12 - closo-carbaborate anions. This study significantly expands the known toolkit of solid-state, poly(carba)borate-based salts capable of superionic conductivities and provides valuable insights into the effect of crystal lattice, unit cell volume, number of carbon atoms incorporated into the anion, and charge polarization on ionic conductivity.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Transforming MOFs for energy applications using the guest@MOF concept

As the world transitions from fossil fuels to clean energy sources in the coming decades, many technological challenges will require chemists and material scientists to develop new materials for applications related to energy conversion, storage, and efficiency. Because of their unprecedented adaptability, metal–organic frameworks (MOFs) will factor strongly in this portfolio. By utilizing the broad synthetic toolkit provided by the fields of organic and inorganic chemistry, MOF pores can be customized to suit a particular application. Of particular importance is the ability to tune the strength of the interaction between the MOF pores and guest molecules. By cleverly controlling these MOF–guest interactions, the chemist may impart new function into the Guest@MOF materials otherwise lacking in vacant MOF. Herein, we highlight the concept of the Guest@MOF as it relates to our efforts to develop these materials for energy-related applicatons. Additionally, our work in the areas of H 2 and noble gas storage, hydrogenolysis of biomass, light-harvesting, and conductive materials will be discussed. Of relevance to light-harvesting applications, we report for the first time a postsynthetic modification strategy for increasing the loading of a light-sensitive electron-donor molecule in the pores of a functionalized MIL-101 structure. Through the demonstrated versatility of these approaches, we show that, by treating guest molecules as integral design elements for new MOF constructs, MOF science can have a significant impact on the advancement of clean energy technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Improved Treatment of 1–4 Interactions in Force Fields for Molecular Dynamics Simulations

Traditional force fields commonly use a combination of bonded torsional terms and empirically scaled nonbonded interactions to capture 1-4 energies and forces of atoms separated by three bonds in a molecule. While this approach can yield accurate torsional energy barriers, it often leads to inaccurate forces and erroneous geometries and creates an interdependence between dihedral terms and nonbonded interactions, complicating parametrization and reducing transferability. Here, in this paper, we demonstrate that 1-4 interactions can be accurately modeled using only bonded coupling terms, eliminating the need for arbitrarily scaled nonbonded interactions altogether. Furthermore, by leveraging the automated parametrization capabilities of the Q-Force toolkit, we efficiently determine the necessary coupling terms without the need for manual adjustment. Our approach is first validated on a range of small molecule systems, encompassing both flexible and rigid structures, and shows a significant improvement in force field accuracy, obtaining subkcal/mol mean absolute error for every molecule tested. We further extend the bonded-only model for 1-4 interactions to Amber ff14sb, CHARMM36, and OPLS-AA force fields to reproduce ab initio gas and implicit solvent ϕ,ψ surfaces of alanine dipeptide.

Abdullah, Aalim S. [University of California, Berk↗
DOE OSTI2018

Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations

Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin–protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co 3+ , Co 2+ , and Co 1+ , and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. In conclusion, the approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

New Instrument for Time-Resolved OH and HO 2 Quantification in High-Pressure Laboratory Kinetics Studies

Here, we have constructed a new time-resolved high-pressure fluorescence assay by gas expansion (HP-FAGE) apparatus, optimized for the detection of OH and HO 2 radicals in complex gas-phase reactions. The new instrument fills a gap in the existing experimental toolkit for chemical kinetics by enabling the quantification of two key reactive species with microsecond time resolution from high-pressure sources, which was previously not attainable. The HP-FAGE is interfaced with a flow reactor, designed for pressures up to 100 bar and temperatures up to 1000 K, in which reactions are initiated by laser photolysis of radical precursors at repetition rates of 1–10 Hz. The HP-FAGE samples gas out of the reactor into a miniature FAGE chamber, where OH is detected by resonant laser-induced fluorescence using a time-delayed probe laser pulse. HO 2 is converted to OH via reaction with NO and then detected by OH fluorescence. The novel FAGE design places the probe region very close to the gas expansion, minimizing the transport time of sampled molecules and resulting in time resolution better than 20 μs for both OH and HO 2 . We calibrate the sensitivity of HP-FAGE, validate its performance with measurements of well-known reaction kinetics (OH + CH 4 , OH + OH, OH + HO 2 , and HO 2 + HO 2 ), and discuss prospects for its future use.

calibration↗
DOE OSTI2025

Resolving the Coverage Dependence of Surface Reaction Kinetics with Machine Learning and Automated Quantum Chemistry Workflows

Microkinetic models for catalytic systems require estimation of many thermodynamic and kinetic parameters that can be calculated for isolated species and transition states using ab initio methods. However, the presence of nearby coadsorbates on the surface can dramatically alter these thermodynamic and kinetic parameters causing them to be dependent on species coverage fractions. As there are combinatorially many coadsorbed configurations on the surface, computing the coverage dependence of these parameters is far less straightforward. We present a framework for generating and applying machine learning models to predict coverage-dependent parameters for microkinetic models. Our toolkit enables automatic calculation and evaluation of coadsorbed configurations allowing us to sample 2,000 coadsorbed adsorbates and transition states (TSs) for a diverse set of 9 reactions on Cu(111), a challenging surface, with four possible coadsorbates. This dataset was then used to train subgraph isomorphic decision trees (SIDTs) to predict the stability and association energy of configurations. We were able to achieve mean absolute errors (MAEs) of 0.106 eV on adsorbates, 0.172 eV on TSs, and due to natural error cancellation in SIDTs for relative properties, 0.130 eV on reaction energies and 0.180 eV on activation barriers. In conclusion, we describe how to use these models to predict coverage-dependent corrections for adsorbates and TSs and demonstrate on H*, HO*, and O* comparing the generated SIDT model with an iteratively refined version.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Bottom-Up Simulation, Reconstruction, and Quantification of Macromolecule Sequences from Experimental Polymerizations

Motivated by the canonical sequence–structure–function paradigm, tools to characterize chemical patterning in natural biomacromolecules, from proteins to nucleic acids, have grown exponentially in recent years. However, analogous strategies for synthetic macromolecules remain in nascent stages, complicated by sequence polydispersity and analytical limitations. To address this, we have developed a comprehensive and open-source Python package, PRISM (polymer rate insights and sequence modeling), an end-to-end workflow that provides a path from experimental kinetics measurements to quantitative and qualitative metrics for describing chemical patterning in stochastic polymers. First, a numerical integration strategy was constructed to simulate and fit experimental data from reversible addition–fragmentation chain transfer (RAFT) polymerization kinetics, enabling the facile estimation of relevant reactivity ratios. These ratios were then used in a mechanism-specific stochastic kinetic simulation strategy to simulate sequence ensembles corresponding to model systems spanning experimental copolymers, classes of statistical polymers (e.g., alternating, block, and gradient), and multiblock copolymers. Lastly, inspired by sequence homology metrics from bioinformatics, we introduce visualization strategies and quantitative metrics to facilitate comparisons of different sequence ensembles. As the sequence–structure–function paradigm becomes increasingly central in de novo design of synthetic macromolecules, this toolkit provides a first step toward accurate and representative sequence description and featurization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Designing a Nanoscale Three-phase Electrochemical Pathway to Promote Pt-catalyzed Formaldehyde Oxidation

Gas-phase heterogeneous catalysis is a process spatially constrained on the two-dimensional surface of a solid catalyst. Here, we introduce a new toolkit to open up the third dimension. We discovered that the activity of a solid catalyst can be dramatically promoted by covering its surface with a nanoscale-thin layer of liquid electrolyte while maintaining efficient delivery of gas reactants, a strategy we call three-phase catalysis. Introducing the liquid electrolyte converts the original surface catalytic reaction into an electrochemical pathway with mass transfer facilitated by free ions in a three-dimensional space. Furthermore, we chose the oxidation of formaldehyde as a model reaction and observed a 25000-times enhancement in the turnover frequency of Pt in three-phase catalysis as compared to conventional heterogeneous catalysis. We envision three-phase catalysis as a new dimension for catalyst design and anticipate its applications in more chemical reactions from pollution control to the petrochemical industry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Correlated Nanoscale Analysis of the Emission from Wurtzite versus Zincblende (In,Ga)As/GaAs Nanowire Core–Shell Quantum Wells

Although the properties of wurtzite GaAs have been extensively researched during the past decade, little is known about the influence of the crystal polytype on ternary (In,Ga)As quantum well structures. We address this concern with a unique combination of correlated, spatially resolved measurement techniques on core–shell nanowires that contain extended segments of both the zincblende and wurtzite polytypes. Cathodoluminescence hyperspectral imaging reveals a blue-shift of the quantum well emission energy by 75 ± 15 meV in the wurtzite polytype segment. Nanoprobe X-ray diffraction and atom probe tomography enable k·p calculations for the specific sample geometry to reveal two comparable contributions to this shift. First, there is a 30% drop in In mole fraction going from the zincblende to the wurtzite segment. Second, the quantum well is under compressive strain, which has a much stronger impact on the hole ground state in the wurtzite than in the zincblende segment. Our findings illustrate the role of the crystal structure in tuning the emission of (In,Ga)As quantum wells and pave the way to exploit the possibilities of three-dimensional band gap engineering in core–shell nanowire heterostructures. At the same time, we have demonstrated an advanced characterization toolkit for the investigation of semiconductor nanostructures.

(In,Ga)As quantum well↗
DOE OSTI2022

Kinetic Probes of the Origin of Activity in MOF-Based C–H Oxidation Catalysis

The development of homogeneous catalysis is enabled by the availability of a rich toolkit of kinetics experiments, such as the Hgdrop test, that differentiate catalytic activity at ligand-supported metal complexes from potential heterogeneous catalysts derived from decomposition of molecular species. Metal-organic frameworks (MOFs) have garnered significant attention as platforms for catalysis at site-isolated, interstitial catalyst sites. Unlike homogeneous catalysis, relatively few strategies have been advanced to evaluate the origin of catalytic activity in MOF-promoted reactions. Many of the MOFs that have been examined as potential catalysts are comprised of molecular constituents that represent viable catalysts in the absence of the extended MOF lattice, and thus interfacial sites and leached homogeneous species represent potential sources of catalyst activity. Here, we demonstrate that analysis of deuterium kinetic isotope effects (KIEs) and olefin epoxidation diastereoselectivity provides probes of the origin of catalytic activity in MOF-promoted oxidation reactions. These analyses support involvement of lattice-based Fe sites in the turnover-limiting step of C–H activation with Fe-MOF-74-based materials (i.e., the MOF functions as a bona fide catalyst) and evidence that Cu 2 -based MOF MIL-125-Cu 2 O 2 functions as a solid-state initiator for solution-phase oxidation chemistry and is not involved in the turnover limiting step (i.e., the MOF does not function as a catalyst for substrate functionalization). furthermore, we anticipate that the simple experiments described here will provide a valuable tool for clarifying the role of MOFs in C–H oxidation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

In situ Stress Monitoring Reveals Tension and Wrinkling Evolutions during Halide Perovskite Film Formation

Metal halide perovskites (MHPs) are promising candidates for next-generation thin film photovoltaics and high-performance tandems. Solution-processed MHP films are susceptible to residual stress that can induce undesirable surface wrinkles. However, the origins and evolution of stress during solution processing remain elusive. Here, in this work, we utilize multimodal in situ characterizations, including substrate curvature, reflectance, absorbance, and photoluminescence, to monitor stress and morphology evolution during MHP film formation. A film formation model emerges, consisting of a perovskite top crust on a semirigid sol with the ability to transfer mechanical forces. The phase transformation induces tension in the MHP crust, while shrinkage of the sol causes additional compression and surface wrinkles. Wrinkle-free films are formed through dynamically balancing forces between the crust and the sol. This study provides a powerful toolkit for the fast-growing area of stress engineering in MHP photovoltaics to achieve dynamic control of film stress and surface morphology.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Controlling the Crystal Packing and Morphology of Metal–Organic Macrocycles through Side-Chain Modification

Supramolecular nanotubes constructed from the self-assembly of conjugated metal–organic macrocycles provide a unique collection of materials properties, including solution processability, porosity, and electrical conductivity. Here we show how small modifications to the macrocycle periphery subtly alter the noncovalent interactions governing self-assembly, leading to large changes in crystal packing, crystal morphology, and materials properties. Specifically, we synthesized five distinct copper-based macrocycles that differ in either the steric bulk, polarity, or hydrogen-bonding ability of the peripheral side chains. We show that the electrical conductivity of these macrocycles is highly sensitive to steric bulk, decreasing by 3 orders of magnitude upon introduction of peripheral neopentyl substituents. Here, we further show that the introduction of hydrogen-bonding groups leads to more ordered packing and a dramatic increase in crystallite size. Together, these results establish side-chain engineering as a rich toolkit for controlling the packing structure, particle morphology, and bulk properties of conjugated metal–organic macrocycles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Orthogonal Degron System for Controlled Protein Degradation in Cyanobacteria

Synechococcus elongatus PCC 7942 is a model cyanobacterium for study of the circadian clock, photosynthesis, and bioproduction of chemicals, yet nearly 40% of its gene identities and functions remain unknown, in part due to limitations of the existing genetic toolkit. While classical techniques for the study of genes (e.g., deletion or mutagenesis) can yield valuable information about the absence of a gene and its associated protein, there are limits to these approaches, particularly in the study of essential genes. In this research, we developed a tool for inducible degradation of target proteins in S. elongatus by adapting a method using degron tags from the Mesoplasma florum transfer-messenger RNA (tmRNA) system. We observed that M. florum lon protease can rapidly degrade exogenous and native proteins tagged with the cognate sequence within hours of induction. We used this system to inducibly degrade the essential cell division factor, FtsZ, as well as shell protein components of the carboxysome. Our results have implications for carboxysome biogenesis and the rate of carboxysome turnover during cell growth. Lon protease control of proteins offers an alternative approach for the study of essential proteins and protein dynamics in cyanobacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Engineering an Extremely Hybrid PKS for Adipic Acid Production

Polyketide synthases (PKSs) are modular enzymes with exceptional potential as biocatalysts for producing non-native compounds. Here, we report the first PKS-based pathway for adipic acid (AA), an industrial monomer for nylon production, by engineering one of the most extensively hybridized PKS systems to date. Using a retrobiosynthetic approach, we identified EtnB, a succinyl-CoA-loading module that uniquely retains the terminal carboxyl group, enabling access to dicarboxylic polyketide products, rarely produced by canonical PKSs. EtnB was coupled to a fully reducing extension module through an engineered communication linker, which improved ACP–KS interactions, enhanced titers, and demonstrated selective succinyl-CoA loading in vivo . This construct integrates genes from five organisms─with domains from seven PKS modules joined across six non-natural junctions─and functions in both Escherichia coli and Pseudomonas putida . Additional engineering that included AT domain exchanges, optimization of extender unit supply, and host strain metabolic rewiring further increased AA production. Together, this work demonstrates that highly chimeric PKSs can be rendered functional through rational design, expands the PKS toolkit with a carboxyl-retaining loading module, and establishes a versatile platform for engineering diacids and other noncanonical products through PKS pathways.

biomanufacturing↗
DOE OSTI2026

Quantitative Dissection of Agrobacterium Virulence to Generate a Synthetic Ti Plasmid

Agrobacterium is not only a costly plant pathogen but is also an essential tool for plant transformation. Though Agrobacterium-mediated transformation (AMT) has been heavily studied, its polygenic nature and complex transcriptional regulation make identification of the genetic basis of transformational efficiency difficult through traditional genetic and bioinformatic approaches. Here, we use a bottom-up synthetic approach to systematically engineer the tumor-inducing plasmid (pTi), wherein the majority of virulence machinery is encoded. Using a validated toolkit to control Agrobacterium gene expression in planta, we perform a quantitative dissection of AMT to investigate the contributions of critical vir-genes at different expression levels. We construct a synthetic pTi capable of transient plant and stable fungal transformation and characterize bottlenecks and solutions for complex polygenic synthetic pTi designs. Our reductionist approach demonstrates how bottom-up engineering can be used to dissect and elucidate the genetic underpinnings of complex biological traits, laying the foundation for future engineering to establish full synthetic control over the critical process of AMT.

Agrobacterium-mediated transformation↗