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DOE OSTI2025

Multi-phase characterization of pitch-carbon coated nano-silicon anodes for lithium-ion batteries

Silicon (Si) is a leading next-generation Li-ion battery anode candidate that meets rigorous performance demands for portable power including enhanced power and energy density with robust cycling performance. However, a series of complex and interrelated reactions lead to reduced calendar life in Si-containing systems and therefore challenge practical adoption. In the present work, we probe the mechanisms underlying observed performance improvements by adding a pitch-carbon coating onto nano-Si material. We pair solid-phase (X-ray photoemission spectroscopy, Fourier-transform infrared), semi-volatile phase (solid-phase microextraction-gas chromatography-mass spectrometry), and gas-phase (gas chromatography-flame-ionization detector) characterization signals to comprehensively evaluate the impact of pitch-carbon coating on the evolution of the Si solid-electrolyte interphase (SEI) and the associated impacts on electrode/electrolyte reactivity. The pitch-carbon is found to serve as a physicochemical barrier, reducing the electro-active surface area for Si/electrolyte reactivity and preventing Si oxidation. Further, the pitch-carbon coating promotes the evolution of a more-favorable SEI by subsuming substantial functionality typically associated with the fluoroethylene carbonate (FEC) electrolyte additive - such as alkoxide scavenging and suppression of transesterification pathways - and by shifting the competitive electrolyte degradation pathways' favorability. The multi-phase characterization approach enables holistic end-products evaluation from complex (electro)chemical interfacial reactions, which informs a robust interpretation of the carbon coating's role in electrochemical performance improvements. The present mechanistic evaluation aids the rational design for improved nano-Si materials.

25 ENERGY STORAGE↗

DOE OSTI2025

Active-noise-induced dynamic clustering of passive colloidal particles

Active fluids generate spontaneous, often chaotic mesoscale flows. Harnessing these flows to drive soft materials embedded within an active fluid into structures with controlled length scales and lifetimes is a key challenge at the interface between the fields of active matter and nonequilibrium self-assembly. Here, we present a simple and efficient computational approach to model soft materials advected by active fluids, by simulating particles moving in a spatiotemporally correlated noise field. To illustrate our approach, we simulate the dynamical self-organization of repulsive colloids within such an active noise field. The colloids form structures whose sizes and dynamics can be tuned by the correlation time and length of the active fluid, and range from small rotating droplets to clusters with internal flows and system-spanning sizes that vastly exceed the active correlation length. Our results explain how the interplay between active fluid time and length scales and emergent driven assembly can be used to rationally design functional assemblies. More broadly, our approach can be used to efficiently simulate diverse active fluids and other systems with spatiotemporally correlated noise.

Brownian dynamics↗

DOE OSTI2022

Energy-Efficient Microbial Electrochemical Lignin and Alkaline Hydroxide Recovery from DMR Black Liquor

Black liquor is a complex waste stream generated from the fast-expanding biorefinery industry, and the high management cost has been known as a major development barrier. In this work, we demonstrated a rationally designed 4-chamber microbial electrolysis process that was capable of recovering the value-added lignin, NaOH, and H2 products while removing waste organics from the Deacetylation and Mechanical Refining (DMR) black liquor, which could potentially reduce the disposal cost by up to 40%. The lab-scale MEC achieved 52% organic removal from a highly concentrated feedstock (28,960 ± 212 mg/L COD) and recovered 83.2 mM NaOH under a small voltage application (1.2 V). Lignin recovery was observed to be as high as 13.98 +/- 0.28 g/L, and 0.35 L/L/day H2 was produced with a faradaic efficiency of 93.5%. This work provided a good example on how complex liquid waste stream can be valorized via multi-functional microbial electrochemical technology, and how the traditionally unfavored pH gradient in an electrochemical reactor can be manipulated for lignin precipitation and alkaline recovery at the same time. The versatility and good performance in concurrent contaminants removal, lignin precipitation, H2 production and NaOH recovery demonstrate a good potential for microbial electrolysis in black liquor treatment.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗

DOE OSTI2026

Conserving asphalt resources: Rethinking rejuvenator performance evaluation through peptizing efficiency

Timely rejuvenation and restoration of asphalt are essential conservation practices that help preserve and extend the service life of roads, bridges, driveways, and parking lots. The performance of asphalt rejuvenators is often assessed based on their diffusion rates and softening power, yet these metrics alone fail to capture true rejuvenation potential. Here, this study integrates density functional theory (DFT) modeling with experimental analysis to show that rejuvenation effectiveness is primarily governed by molecular interactions with oxidized asphaltene nanoaggregates. DFT results revealed that amide- and unsaturated-chain compounds, such as hexadecanamide, oleic acid, and 9,17-octadecadienal, act cooperatively to disrupt π–π stacking and exfoliate asphaltene layers, reducing binding strength and enhancing dispersion. Unlike bulky, rigid molecules that remain trapped, these components remain mobile and repeatedly interact with multiple aggregation sites. Experimental validation using rheometry and FTIR confirmed that such molecularly compatible rejuvenators restore the binder flexibility and polydispersity, even when diffusion is relatively slow. Building on this mechanistic foundation, six rejuvenators (A2, A5, A7, A8, A9, and A10) were evaluated using a three-metric performance framework encompassing cracking resistance (Glover–Rowe parameter), UV stability, and surface hydrophobicity. Among the six rejuvenators evaluated, A9 exhibited the highest overall performance, reducing the Glover–Rowe cracking parameter by 85% (from 351 kPa to 53 kPa), demonstrating the greatest resistance to UV-induced aging with a stability index of 4.17 h·kPa⁻¹, and increasing surface hydrophobicity to a contact angle of 103.6°. Its superior performance is primarily attributed to its amide- and unsaturated-chain components, which act cooperatively to disrupt π–π stacking interactions and exfoliate asphaltene layers, thereby promoting molecular deagglomeration and enhancing long-term durability. These results shift the criteria for selecting rejuvenators: effective candidates must pair the electronic capability to unlock aged asphaltenes with sufficient structural stability to resist secondary aging and restore hydrophobicity. Restoring hydrophobicity is critical, as aging reduces the asphalt’s water repellency and increases water diffusion, which in turn accelerates moisture-related damage; consequently, a high-performing rejuvenator must effectively restore the binder’s hydrophobic characteristic. Collectively, these findings provide a framework for the rational design of next-generation of bio-based rejuvenators that enhance pavement longevity and promote long-term sustainability.

Aging↗

DOE OSTI2020

An activatable NIR fluorescent rosol for selectively imaging nitroreductase activity

Hypoxia (i.e., pO 2 ≤ ~1.5 %) is an important characteristic of tumor microenvironments that directly correlates with resistance against first-line therapies and tumor proliferation/infiltration. The ability to accurately identify hypoxic tumor cells/tissue could afford tailored therapeutic regimens for personalized treatment, the development of more-effective therapies, and discerning the mechanisms underlying disease progression. Fluorogenic constructs currently developed for identifying such tumor cells/tissue operate by targeting the bioreductive activity of primarily the nitroreductase (NTR) class of enzymes, but collectively such constructs unfortunately present photophysical and/or physicochemical shortcomings that could limit their effectiveness upon implementation. To overcome these limitations, we present the rational design, development, and evaluation of the first activatable ultracompact xanthene core-based molecular probe (NO 2 -Rosol) for selectively imaging NTR activity that affords an “OFF-ON” near-infrared (NIR) fluorescence response (ca. > 700 nm) alongside a remarkable Stokes shift (ca. > 150 nm) via NTR activity-facilitated modulation to its energetics whereby the resultant interplay discontinues an intramolecular d-PET fluorescence-quenching mechanism transpiring between directly-linked electronically-uncoupled π-systems comprising its components. DFT calculations guided selection of a suitable fluorogenic scaffold and nitroaromatic moiety candidate that when adjoined could (i) afford such photophysical response upon bioreduction by upregulated NTR activity in hypoxic tumor cells/tissue and (ii) employ a retention mechanism strategy that capitalizes on an inherent physical property of the NIR fluorogenic scaffold for achieving signal amplification. NO 2 -Rosol demonstrated 705 nm NIR fluorescence emission and a 157 nm Stokes shift, selectivity for NTR over relevant bioanalytes, and a 28- and 12-fold fluorescence enhancement in solution and between cells cultured under different oxic conditions, respectively. Finally, in establishing feasibility for NO 2 -Rosol to provide favorable contrast levels in in solutioand in vitrostudies, we anticipate NO 2 -Rosol similarly doing so in future studies towards its translation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

First-principles elucidation of the effects of Al-doping on Li-ion diffusion in LiCoO 2

Al-doped garnet Li 7 La 3 Zr 2 O 12 solid-electrolyte and LiCoO 2 cathode are promising choices as catholyte materials in all solid-state Li batteries, however, interdiffusion of Al is commonly evident during high-temperature processing and electrochemical cycling. Furthermore, to address the impact of Al interdiffusion on Li + transport properties in LiCoO 2 , we carried out a systematic evaluation of Al doping on Li + diffusion barriers in LiCoO 2 using first-principles based methods. Following the monovacancy diffusion mechanism, Al-doping (primarily at the Co site) is found to improve Li diffusion kinetics in the LiCoO 2 lattice due to favorable CoO 6 octahedral distortion experienced at the transition states. However, when considering the previously established dominant divacancy diffusion mechanism, slower Li diffusion is generally expected. In addition, a broad variation of Li diffusion barriers is observed upon Al doping, which suggests the system may suffer from non-uniform Li incorporation and diffusion that adversely affects its rate capacity during cycling. In summary, this work highlights, for the rational design of catholyte of all solid-state batteries, special attention may need to be paid to address the potential impact of non-intentional doping induced during processing on the overall electrochemical performance of the catholyte.

Al-doped LiCoO2↗

DOE OSTI2021

Wolffia, a minimalist plant and synthetic biology chassis

A highly simplified species for genome engineering would facilitate rational design of a synthetic plant. A candidate species is the aquatic, non-grass monocot wolffia (Wolffia australiana) in the Lemnaceae family. Commonly known as watermeal, wolffia is a rootless ball of several thousand cells the size of a pinhead and the fastest growing plant known on Earth. Its extreme morphological reduction is coupled to transposon-mediated streamlining of its transcriptome, which represents a core set of nonredundant protein coding genes. Despite its body plan and transcriptome being highly specialized for continuous growth, wolffia retains cell types relevant to higher plants. Finally, systems level studies with this species could enable the creation of a defined biological chassis for synthetic plant construction.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Glass-fiber-reinforced polymeric film as an efficient protecting layer for stable Li metal electrodes

With numerous reports on protecting films for stable lithium (Li) metal electrodes, the key attributes for how to construct these efficient layers have rarely been fully investigated. Here, we report a rationally designed hybrid protective layer (HPL) with each component aligning with one key attribute; i.e., cross-linked poly(dimethylsiloxane) (PDMS) enhances flexibility, polyethylene glycol (PEG) provides homogeneous ion-conducting channels, and glass fiber (GF) affords mechanical robustness. A significant improvement of the electrochemical performance of HPL-modified electrodes can be achieved in Li/HPL@Cu half cells, HPL@Li/HPL@Li symmetric cells, and HPL@Li/LiFePO 4 full cells. Even with an industrial standard LiFePO 4 cathode (96.8 wt % active material), the assembled cell still exhibits a capacity retention of 90% after 100 cycles at 1 C. More importantly, the functionality of each component has been studied comprehensively via electrochemical and physical experiments and simulations, which will provide useful guidance on how to construct efficient protective layers for next-generation energy storage devices.

25 ENERGY STORAGE↗

DOE OSTI2021

Quantifying lithium loss in amorphous silicon thin-film anodes via titration-gas chromatography

Silicon with a high theoretical capacity (3,579 mAh/g) is a promising anode candidate for lithium-ion batteries. However, commercialization is still impeded by low Coulombic efficiency, caused by solid electrolyte interphase (SEI) formation and trapped lithium (Li)-silicon (Si) alloy during repeated volume change. Quantifying capacity losses from each factor is crucial to formulate rational design strategies for further improvement. In this work, titration-gas chromatography and cryogenic transmission electron microscopy are applied to characterize the evolution of trapped Li-Si alloy and SEI growth in a silicon thin-film anode. It is found that continuous growth of the SEI is the dominant factor for lithium inventory loss during cycling, with only a marginal increase in trapped Li-Si alloy. This study offers a quantitative approach to differentiate Li in the SEI from trapped Li in Li-Si alloy through a silicon thin-film anode, providing unique insights into identifying critical bottlenecks for developing Si anodes.

25 ENERGY STORAGE↗

DOE OSTI2023

High-strength, lightweight nano-architected silica

Continuous nanolattices are an emerging class of mechanical metamaterials that are highly attractive due to their superior strength-to-weight ratios, which originate from their spatial architectures and nanoscale-sized elements possessing near-theoretical strength. Rational design of frameworks remains challenging below 50 nm because of limited methods to arrange small elements into complex architectures. Here, we fabricate silica frameworks with ~4- to 20-nm-thick elements using self-assembly and silica templating of DNA origami nanolattices and perform in situ micro-compression testing to examine the mechanical properties. We observe strong effects of lattice dimensions on yield strength (σ $\mathcal{y}$ ) and failure mode. Silica nanolattices are found to exhibit yield strengths higher than those of any known engineering materials with similar mass density. The robust coordination of the nanothin and strong silica elements leads to the combination of lightweight and high-strength framework materials offering an effective strategy for the fabrication of nanoarchitected materials with superior mechanical properties.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Discerning structure sensitivity of Ni-core Pd-shell nanoparticles for enhanced nitrite reduction

Denitrification using Pd-based catalysts converts N-oxyanions into harmless products. However, the metal cost and scarcity are barriers to application. In this work, we synthesize water-suspended, structure-controlled Ni-core/Pd-shell nanoparticles (Ni@Pd NPs) that show Pd-catalyzed nitrite (NO 2 − ) reduction catalysis promoted by Ni. The NPs immobilized on Al 2 O 3 (0.47 wt % Pd and 0.74 wt % Ni) have higher NH 4 + selectivity and higher catalytic activity than wet-impregnated Pd/Al 2 O 3 (1.0 wt % Pd), i.e., 315.4 vs. 132.1 Lg surface Pd −1 min −1 . X-ray photoelectron spectroscopy (XPS) and CO-diffuse reflectance infrared Fourier transform spectroscopy (CO-DRIFTS) analyses show that Ni increases Pd electron density, which is proposed to lower the bond dissociation energy barrier for nitric oxide surface intermediate. Low-coordinated Pd atoms correlate to high activity and low NH 4 + selectivity. Using CatCost software, we estimate Ni@Pd/Al 2 O 3 to have a ∼40% lower manufacturing cost compared to wet-impregnated Pd/Al 2 O 3 . This rationally designed catalyst illustrates how nickel promotes Pd catalysis and how Pd usage can be lowered for denitrification and other hydrogenation reactions.

CO-DRIFTS↗

DOE OSTI2022

MEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supply

Isoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. It has been reported that IPP and DMAPP feedback-regulate the activity of deoxyxylulose 5-phosphate synthase (DXS), a dimeric enzyme that catalyzes the main flux-controlling step of the MEP pathway. Here we provide experimental insights into the underlying mechanism. Isothermal titration calorimetry and dynamic light scattering approaches showed that IPP and DMAPP can allosterically bind to DXS in vitro, causing a size shift. In silico ligand binding site analysis and docking calculations identified a potential allosteric site in the contact region between the two monomers of the active DXS dimer. Modulation of IPP and DMAPP contents in vivo followed by immunoblot analyses confirmed that high IPP/DMAPP levels resulted in monomerization and eventual aggregation of the enzyme in bacterial and plant cells. Loss of the enzymatically active dimeric conformation allows a fast and reversible reduction of DXS activity in response to a sudden increase or decrease in IPP/DMAPP supply, whereas aggregation and subsequent removal of monomers that would otherwise be available for dimerization appears to be a more drastic response in the case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our results represent an important step toward understanding the regulation of the MEP pathway and rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Zinc chloride affects chondrogenesis via VEGF signaling

Highlights: • ZnCl2 increases expression of various chondrogenic signaling intermediates. • VEGF/VEGFR play a key role in modulating levels of chondrogenesis. • Insulin mimetics are an appealing option for improvement of fracture healing. • Axitinib + ZnCl2 treatment results in decreased transcription of chondrogenic genes. Insulin mimetics, including zinc containing compounds, have previously been shown to influence chondrogenesis as it relates to healing of fractures in various preclinical models. However, the mechanism by which these compounds drive chondrogenic differentiation is yet undefined. Here, via next-generation sequencing (NGS) and in vitro functional validation, we show that Zinc Chloride (ZnCl{sub 2}) induces expression of both chondrogenic genes (Sox9, Runx1, collagen) as well as genes associated with VEGF-mediated signal transduction, including VEGF receptors 1 and 2 and their ligands; VEGF-A and VEGF-B. Noticeably, although insulin was able to also induce expression of these pro-angiogenic and pro-chondrogenic genes, the impact of insulin on expression of VEGF receptor and ligand genes was marginal when compared to that of ZnCl{sub 2.} Furthermore, while the VEGFR antagonist, Axitinib, was able to attenuate the pro-chondrogenic effects of both insulin and ZnCl{sub 2}; a reduction in gene and protein expression was most profoundly observed when the antagonist was applied to cells treated with ZnCl{sub 2.} Taken together, these data suggest an important role for the VEGF-mediated signal transduction pathways in the positive effects observed when applying zinc-based compounds as adjuvants for chondrogenesis-mediated fracture healing. In this regard, further mechanistic evaluation of ZnCl{sub 2} and other zinc-containing insulin mimetics may support rational design of therapies targeted for disease indications associated with impaired fracture healing.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Atomic-scale Imaging of PGM-free Catalyst Active Sites by 30 keV 4D-STEM

Platinum group metal (PGM)-free catalysts have attracted a large amount of attention due to their potential for enabling low-cost, commercially viable hydrogen fuel cells and electrolyzers [1]. Degradation of cell performance remains a significant challenge, however, currently limiting implementation of devices that utilize PGM-free materials [2]. Controlling degradation in these materials requires a better understanding of the atomic structure of active sites, thought to be FeN4 structures within a graphitic carbon lattice, which would enable more accurate prediction of the associated degradation pathways. The exact structural arrangement of active sites in these materials is still debated since a range of structures have been computationally predicted and methods to directly validate these models are still needed [1,3-5].While scanning transmission electron microscopy (STEM) has provided initial glimpses into the nature of the proposed active sites, detailed evaluation of the structure of these sites is challenging since they involve defects, edges, and nitrogen dopants in the graphitic lattice, which are susceptible to beam damage [6,7]. Conventional STEM imaging and spectroscopy methods exacerbate this problem with dose-inefficiency or nonideal contrast characteristics for imaging light and heavy elements simultaneously. A method that minimizes damage while generating dose-efficient, easily-interpretable contrast for both light and heavy elements is therefore needed to facilitate imaging of sensitive active site atomic structure.Here, we demonstrate direct atomic-scale imaging of PGM-free catalyst active sites by low-voltage four-dimensional (4D)-STEM. To accomplish this, we pair a 30 keV aberration-corrected probe, which minimizes knock-on damage, with a fast pixelated detector that has optimal performance at low beam energies [8]. We show how this setup enables relatively simple center-of-mass (CoM) techniques [9,10] to produce images with an increased signal-to-noise ratio (SNR) and light-element contrast over conventional imaging modes, allowing the entire active site structure to be imaged at the atomic scale. Moreover, we show how electron ptychography [11,12] enables images with further improved characteristics to be obtained, for example by minimizing residual aberrations, which provides a more accurate structural representation. The increased understanding that these low-voltage 4D-STEM techniques will provide about the atomic structure of PGM-free active sites and their associated degradation pathways will facilitate rational design of next-generation materials, promoting development of low-cost hydrogen fuel cells, electrolyzers, and other energy conversion devices [13]. References:[1] U Martinez et al., Adv. Mater. 31 (2019), p. 1806545.[2] Y Shao et al., Adv. Mater. 31 (2019), p. 1807615.[3] J Kneebone et al., J. Phys. Chem. C 121, (2017), p.16283.[4] T Mineva et al., ACS Catal. 9 (2019), p. 9359.[5] J Li et al., Nat. Catal. 4 (2021), p. 10.[6] T Susi et al., ACS Nano 6 (2012), p. 8837.[7] P Zelenay and DJ Myers, US Department of Energy Hydrogen and Fuel Cells Program 2017 Annual Merit Review and Peer Evaluation Meeting, Washington, DC (2017).[8] H Ryll et al., J. Inst. 11 (2016), p. P04006.[9] K Müller et al., Nat. Commun. 5 (2014), p. 5653.[10] I Lazic et al., Ultramicroscopy 160 (2016), p. 265.[11] H Yang et al., Nat. Commun. 7 (2016), p. 12532.[12] Y Jiang et al., Nature 559 (2018), p. 343. [13] Research sponsored by the Hydrogen and Fuel Cell Technologies Office, Office of Energy Efficiency and Renewable Energy, US Department of Energy (DOE). Research was conducted at the Center for Nanophase Materials Sciences, which is a DOE Office of Science User Facility.

Zachman, Michael↗

DOE OSTI2024

Direct Mapping of Polyclonal Epitopes in Serum by HDX-MS

Elucidating the interactions that drive antigen recognition is central to understanding antibody-mediated protection and is vital for the rational design of immunogens. Often, structural knowledge of epitopes targeted by antibodies is derived from isolated studies of monoclonal antibodies, for which numerous structural techniques exist. In contrast, there are very few approaches capable of mapping the full scope of antigen surfaces targeted by polyclonal sera through the course of a natural antibody response. Here, in this study, we develop an approach using immobilized antigen coupled to hydrogen/deuterium exchange with mass spectrometry (HDX-MS) to probe epitope targeting in the context of the fully native serum environment. Using the well-characterized Staphylococcal enterotoxin B (SEB) as a model system, we show that complex combinations of epitopes can be detected and subtle differences across different anti-sera can be discerned. This work reveals new insight into how neutralizing antibodies and antisera target SEB, and more importantly, establishes a novel method for directly mapping the epitope landscape of polyclonal sera.

antigens↗

DOE OSTI2025

Rapid Screening of Single-Atom Catalyst Synthesis Conditions Using ToF-SIMS and Facet-Dependent Single-Crystal Substrates

Single-atom catalysts (SACs) offer superior catalytic performance compared to traditional nanoparticle catalysts but are challenging to develop because of the need for extensive optimization and specialized characterization techniques. Here, this study presents a rapid and versatile method for detecting synthesis conditions and elucidating deposition mechanisms of SACs on various substrates. By depositing active elements (Au, Cu, Ni and Rh) on facet-specific single-crystalline substrates (CeO 2 , TiO 2 , MgO and Al 2 O 3 ) and employing time-of-flight secondary ion mass spectroscopy (ToF-SIMS), we assessed facet-dependent deposition behaviors and identified optimal conditions for solution-based SAC synthesis. On CeO 2 and TiO 2 , we confirmed facet-dependent deposition, primarily influenced by oxygen vacancy density and photocatalytic activity, respectively. MgO exhibited the formation of metal oxide/hydroxide clusters for all active elements, and the degree of clustering for Cu and Ni was correlated with the facet hydrolysis susceptibility. Notably, Au and Rh deposition on MgO was facet-independent, attributed to the formation of hydroxide species in solution. Al 2 O 3 , due to its chemical stability and lack of surface defects, did not show active element deposition. This study not only provides a time and cost-efficient method for prescreening SAC synthesis conditions, but it also provides valuable insights into the various deposition mechanisms governing SAC formation on different substrates, paving the way for the rational design of tailored SACs for various catalytic applications.

ToF-SIMS↗

DOE OSTI2021

The Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair

Enzymes have in vivo life spans. Analysis of life spans, i.e., lifetime totals of catalytic turnovers, suggests that nonsurvivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme life span might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements are lacking: there are too few measurements of in vivo life span, and existing information about the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach for identifying, predicting, and validating instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability and could change our thinking about which enzymes die young in vivo, and why.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes

Peptoids (N-substituted glycines) are a group of highly controllable peptidomimetic polymers. Amphiphilic diblock peptoids have been engineered to assemble crystalline nanospheres, nanofibrils, nanosheets, and nanotubes with biochemical, biomedical, and bioengineering applications. The mechanical properties of peptoid nanoaggregates and their relationship to the emergent self-assembled morphologies have been relatively unexplored and are critical for the rational design of peptoid nanomaterials. In this work, we consider a family of amphiphilic diblock peptoids consisting of a prototypical tube-former (Nbrpm6Nc6, a NH 2 -capped hydrophobic block of six N-((4-bromophenyl)methyl)glycine residues conjugated to a polar NH 3 (CH 2 ) 5 CO tail), a prototypical sheet-former (Nbrpe6Nc6, where the hydrophobic block comprises six N-((4-bromophenyl)ethyl)glycine residues), and an intermediate sequence that forms mixed structures ((NbrpeNbrpm)3Nc6). We combine all-atom molecular dynamics simulations and atomic force microscopy to determine the mechanical properties of the self-assembled 2D crystalline nanosheets and relate these properties to the observed self-assembled morphologies. We find good agreement between our computational predictions and experimental measurements of Young’s modulus of crystalline nanosheets. A computational analysis of the bending modulus along the two axes of the planar crystalline nanosheets reveals bending to be more favorable along the axis in which the peptoids stack by interdigitation of the side chains compared to that in which they form columnar crystals with π-stacked side chains. Here, we construct molecular models of nanotubes of the Nbrpm6Nc6 tube-forming peptoid and predict a stability optimum in good agreement with experimental measurements. A theoretical model of nanotube stability suggests that this optimum is a free energy minimum corresponding to a “Goldilocks” tube radius at which capillary wave fluctuations in the tube wall are minimized.

36 MATERIALS SCIENCE↗