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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Static and Dynamic Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature with Path Integral Simulations at Ambient Temperature

It is a common practice in ab initio molecular dynamics (AIMD) simulations of water to use an elevated temperature to overcome the overstructuring and slow diffusion predicted by most current density functional theory (DFT) models. The simulation results obtained in this distinct thermodynamic state are then compared with experimental data at ambient temperature based on the rationale that a higher temperature effectively recovers nuclear quantum effects (NQEs) that are missing in the classical AIMD simulations. In this work, we systematically examine the foundation of this assumption for several DFT models as well as for the many-body MB-pol model. Here, we find for the cases studied that a higher temperature does not correctly mimic NQEs at room temperature, which is especially manifest in significantly different three-molecule correlations as well as hydrogen bond dynamics. In many of these cases, the effects of NQEs are the opposite of the effects of carrying out the simulations at an elevated temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Polarized, V-Shaped, and Conjoined Biscoumarins: From Lack of Dipole Moment Alignment to High Brightness

Eleven conjoined coumarins possessing a chromeno[3,4-c]chromene-6,7-dione skeleton have been synthesized via the reaction of electron-rich phenols with esters of coumarin-3-carboxylic acids, catalyzed by either Lewis acids or 4-dimethylaminopyridine. Furthermore, Michael-type addition to angular benzo[f]coumarins is possible, leading to conjugated helical systems. Arrangement of the electron-donating amino groups at diverse positions on this heterocyclic skeleton makes it possible to obtain π-expanded coumarins with emission either sensitive to, or entirely independent of, solvent polarity with large Stokes shifts. Computational studies have provided a rationale for moderate solvatochromic effects unveiling the lack of collinearity of the dipole moments in the ground and excited states. Depending on the functional groups present, the obtained dyes are highly polarized with dipole moments of ~14 D in the ground state and ~20–25 D in the excited state. Strong emission in nonpolar solvents, in spite of the inclusion of a NO 2 group, is rationalized by the fact that the intramolecular charge transfer introduced into these molecules is strong enough to suppress intersystem crossing yet weak enough to prevent the formation of dark twisted intramolecular charge transfer states. Photochemical transformation of the dye possessing a chromeno[3,4-c]pyridine-4,5-dione scaffold led to the formation of a spirocyclic benzo[g]coumarin.

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

Fundamental Insights into Cathode Stability: Linking Compositional Tuning and Local Coordination in Complex Metal Oxides under Aqueous Transformations

Compositional tuning of complex metal oxides in Li-ion battery materials influences their performance as well as their end-of-life behavior, in particular, the tendency to release toxic metal cations in aqueous solution. We modeled ternary variants of a parent LiCoO 2 delafossite structure by varying the metal identity and relative amounts. This yielded ten model formulations of Li(A 4/6 B 1/6 C 1/6 )O 2 , where the material is enriched with the A metal and doped with B and C, with Ni, Mn, Co, Fe, Al, V, and Ti as constituent metals. To assess their stability in aqueous conditions, metal release energetics were calculated using a combination of Density Functional Theory calculations and thermodynamics. Metal release in ternary oxides is dictated by subtle variations in the coordination environment of the leaving group. To identify governing chemical features across diverse compositions with varying local coordination environments, we leverage random forest regression and descriptor importance analysis. A key result is that metal–oxygen orbital hybridization, quantified using a projected density-of-states-derived descriptor, H d/p , provides a physically grounded measure of interaction strength that governs metal release energetics. This refined perspective goes beyond conventional oxidation state considerations and offers more robust insights for materials science. Finally, we model defect surface-bound O 2 dimer formation as a proxy for reactive oxygen species (ROS) generation. The results show that Ni-rich compositions more readily stabilize spin-polarized O 2 dimers, corroborating experimental reports of an increased ROS-driven biological response. In conclusion, our results establish a compositional and electronic basis for metal release and surface oxygen reactivity that form a rationale for complex metal oxide design principles.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Defect-Limited Mobility and Defect Thermochemistry in Mixed A-Cation Tin Perovskites: (CH3NH3)1-xCsxSnBr3

Hybrid organic-inorganic semiconductors crystallizing in the perovskite structure present a significant opportunity for realizing defect-tolerant semiconductors. In this work, we examine the solid solution, (CH3NH3)1-xCsxSnBr3, and identify the thermochemistry dictating the intrinsic carrier concentrations and how local structural distortions influences this electronic behavior. This family of compounds exhibits the expected systematic trend in decreasing optical gap with the cesium to methylammonium A-site mixing ratio, x, in the visible region. However, the carrier mobility, as determined from time-resolved microwave conductivity measurements, trends opposite to that expected from first-principles calculations combined with Boltzmann scattering theory calculations of the carrier mobility. We propose that this is a result of increasing carrier scattering with x in (CH3NH3)1-xCsxSnBr3 due to a significant increase in the carrier density with x. By examining the dependence of the carrier density as a function of x, we infer the compositional-dependence of the average enthalpy and nonconfigurational entropy per defect. While diffraction reveals a cubic aristotypic perovskite structure as a function of x at room temperature, the pair distribution functions obtained from synchrotron X-ray total scattering from these materials are better described by symmetry-adapted displacement modes of the Pm3m crystal structure, which we attribute to a large degree of anharmonic dynamics of the atom positions. This analysis shows that CH3NH3+-rich compositions retain mostly linear Sn-Br-Sn bonding environments through the displacements, while Cs+-rich compositions lead to more significantly bent Sn-Br-Sn environments. We propose that these bent bonding arrangements in Cs-rich compositions yield a higher propensity for defect formation. This also provides a rationale for carrier trapping that gives rise to anomalous microwave transients. Together, these results provide insight into the structure-dynamics-properties relationships in this highly anharmonic system with high amplitude atomic motions and low defect formation energies.

defect thermochemistry↗
DOE OSTI2021

Toward Optimizing Electrospun Nanofiber Fuel Cell Catalyst Layers: Polymer–Particle Interactions and Spinnability

We investigate the effect of the poly(acrylic acid) (PAA) carrier polymer concentration on the microstructure and rheological properties of catalyst inks for electrospun polymer–electrolyte membrane fuel-cell catalyst layers. Characterization of an ink microstructure using oscillatory shear rheology showed that the catalyst particles (platinum on carbon) are significantly agglomerated in the absence of PAA or an ionomer. Both the ionomer and PAA promoted the stability of the particles against agglomeration via electrosteric stabilization by adsorbing onto the particle surface. Increasing the PAA concentration increased the stability of the particles (or reduced the agglomerated structure) due to increasing PAA coverage onto the free surface area of the particles. However, beyond a certain increase in concentration, PAA was found to predominantly remain as an excess free polymer in the ink due to an insufficient free/available surface area on the particles for further PAA coverage. Extensional rheology measurements demonstrated that PAA enhances the extensional viscosities of the inks. Consequently, increasing the PAA concentration in the ink promoted the evolution of uniform nanofibers. However, beyond a certain concentration, a significant increase in the shear viscosities of the inks led to defective fiber morphologies because of the onset of flow instabilities. Electrochemical performance comparisons between catalyst layers with different PAA concentrations showed maximum performance at the PAA concentration that led to the least agglomerated structure of the catalyst, most uniform fiber morphologies, and low concentrations of free (non-adsorbing) PAA in the electrode. These results provide a rationale for optimization of electrospun catalyst nanofibers for both spinnability and electrochemical performance.

25 ENERGY STORAGE↗
DOE OSTI2020

Influence of Carbene and Phosphine Ligands on the Catalytic Activity of Gold Complexes in the Hydroamination and Hydrohydrazination of Alkynes

Through kinetic measurements, catalytic and stoichiometric experiments, and DFT calculations, we compare the catalytic activity of gold complexes supported by a variety of ligands (R 3 P, NHC, CAAC-5, CAAC-6, and BiCAAC) in the hydroamination and hydrohydrazination of alkynes. This study provides a rationale for the superior efficiency of a gold complex bearing a bicyclic (alkyl)(amino) carbene (BiCAAC). We demonstrate that this ligand motif, which is readily available, provides a durable gold catalyst that is able to compete with sophisticated state-of-the-art phosphine and NHC ligands, which feature secondary interaction capabilities.

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

A Review on the Impact of SO 2 on the Oxidation of NO, Hydrocarbons, and CO in Diesel Emission Control Catalysis

A high-efficiency after-treatment technology has been required to meet the increasingly stringent regulations on the emissions of nitrogen oxides (NO x ), hydrocarbons (HCs), and carbon monoxide (CO) exhausts from diesel engine vehicles throughout the world. The diesel oxidation catalyst (DOC) is an indispensable part of a diesel-fueled exhaust system, which mainly functions in the oxidation of unburned HCs and CO to CO 2 and H 2 O (in the case of HCs) and a proportion of NO to NO 2 . However, the DOC will unavoidably be poisoned by trace gaseous SO 2 or accumulated sulfur on the catalyst under real operational conditions and hence impair the overall purification efficiency of the aftertreatment system. There have been significant research efforts from both academia and industry involving sulfur-relevant diesel oxidation chemistry and development of robust sulfur-resistant oxidation catalysts. In this review, we focus on recent advances in the study of SO 2 effects on the catalytic oxidation of NO, HCs, and CO over DOCs, with particular attention to the fundamentals beneath apparent observations of sulfur influence on PGM-based and non-noble metal-based catalysts in the different oxidation reactions. Regeneration methods and design rationale for sulfur-resistant catalysts are also covered. Several challenges in the future research regarding microscopic insights into the SO 2 -influencing mechanism and next-generation sulfur-resistant DOC design are highlighted toward real-world practice.

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

Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome

The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives–3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)–the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.

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

Reversing the Irreversible: Thermodynamic Stabilization of LiAlH 4 Nanoconfined Within a Nitrogen-Doped Carbon Host

A general problem when designing functional nanomaterials for energy storage is the lack of control over the stability and reactivity of metastable phases. Using the high-capacity hydrogen storage candidate LiAlH4 as an exemplar, we demonstrate an alternative approach to the thermodynamic stabilization of metastable metal hydrides by coordination to nitrogen binding sites within the nanopores of N-doped CMK-3 carbon (NCMK-3). The resulting LiAlH 4 @NCMK-3 material releases H 2 at temperatures as low as 126 °C with full decomposition below 240 °C, bypassing the usual Li 3 AlH 6 intermediate observed in bulk. Moreover, >80% of LiAlH 4 can be regenerated under 100 MPa H 2 , a feat previously thought to be impossible. Nitrogen sites are critical to these improvements, as no reversibility is observed with undoped CMK-3. Density functional theory predicts a drastically reduced Al–H bond dissociation energy and supports the observed change in the reaction pathway. Finally, the calculations also provide a rationale for the solid-state reversibility, which derives from the combined effects of nanoconfinement, Li adatom formation, and charge redistribution between the metal hydride and the host.

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

Origins of Photoluminescence Instabilities at Halide Perovskite/Organic Hole Transport Layer Interfaces

Metal halide perovskites are promising for optoelectronic device applications; however, their poor stability under solar illumination remains a primary concern. While the intrinsic photostability of isolated neat perovskite samples has been widely discussed, it is important to explore how charge transport layers—employed in most devices—impact photostability. Here, in this paper, we study the effect of organic hole transport layers (HTLs) on light-induced halide segregation and photoluminescence (PL) quenching at perovskite/organic HTL interfaces. By employing a series of organic HTLs, we demonstrate that the HTL’s highest occupied molecular orbital energy dictates behavior; furthermore, we reveal the key role of halogen loss from the perovskite and subsequent permeation into organic HTLs, where it acts as a PL quencher at the interface and introduces additional mass transport pathways to facilitate halide phase separation. In doing so, we both reveal the microscopic mechanism of non-radiative recombination at perovskite/organic HTL interfaces and detail the chemical rationale for closely matching the perovskite/organic HTL energetics to maximize solar cell efficiency and stability.

14 SOLAR ENERGY↗
DOE OSTI2024

Cryo-EM Structure of the Mnx Protein Complex Reveals a Tunnel Framework for the Mechanism of Manganese Biomineralization

The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O 2 directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from Bacillus sp. strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The ß-sheet–rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxE 3 F 3 cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Furthermore, comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization.

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

Critical Role of Framework Flexibility and Disorder in Driving High Ionic Conductivity in LiNbOCl 4

Understanding Li-ion transport is key for the rational design of superionic solid electrolytes with exceptional ionic conductivities. LiNbOCl 4 is reported to be one of the most highly conducting materials in the recently realized new class of soft oxyhalide solid electrolytes, exhibiting an ionic conductivity of ~11 mS·cm -1 . Here, we apply X-ray/neutron diffraction and pair distribution function analysis - coupled with density functional theory/ab-initio molecular dynamics - to determine a structural model that provides a rationale for the high conductivity that we observe experimentally in this nanocrystalline solid. We show that it arises from unusually high framework flexibility at room temperature. This owes to isolated 1-D [NbOCl 4 ] - anionic chains which exhibit energetically favorable orientational disorder that is - in turn - correlated to multiple, disordered and equi-energetic Li + sites in the lattice. As the Li-ions sample the 3-D energy landscape with a fast predicted diffusion coefficient of 5.1 x 10 -7 cm 2 /s at room temperature (σ i calc = 17.4 mS·cm -1 ), the inorganic polymer chains can reorient or vice versa. The activation energy barrier for Li migration through the frustrated energy landscape is especially reduced by the elastic nature of the NbO 2 Cl 4 octahedra evident from very widely dispersed Cl-Nb-Cl bond angles in AIMD snapshots at 300 K. The phonon spectra are predominantly influenced by Cl vibrations in the low energy range, and there is strong overlap between the framework (Cl, Nb) and Li partial pDOS in the region between 1.2 - 4.0 THz. The framework flexibility is also reflected in a relatively low bulk modulus of 22 GPa. In conclusion, our findings pave the way for investigation of future “flex-ion” inorganic solids and open up a new direction for the design of high conductivity, soft solid electrolytes for all-solid-state batteries.

AIMD↗
DOE OSTI2026

Pseudo–Jahn–Teller Distortion in a One-Dimensional π-Conjugated Polymer

Structural distortions in low-dimensional π-conjugated systems profoundly influence their electronic properties, but the control of such behavior in laterally extended systems remains challenging. Here, in this study, we demonstrate that a one-dimensional conjugated polymer─ poly -(difluorenoheptalene-ethynylene) (PDFHE)─undergoes a pronounced out-of-plane backbone distortion, equivalent to a spontaneous symmetry breaking (SSB) of its mirror symmetry. We synthesized PDFHE on noble metal surfaces and characterized its structure and electronic states using low-temperature scanning tunneling microscopy (STM). Rather than adopting a planar, high-symmetry conformation, PDFHE relaxes into nonplanar isomers stabilized by a pseudo–Jahn–Teller (PJT) distortion having mirror-odd out-of-plane character. The distortion lowers the total energy and increases the band gap, providing a concise rationale for the observed symmetry breaking. Density functional theory calculations corroborate these findings, providing a microscopic explanation for the SSB. Our results show that even in mechanically robust extended π-systems, subtle electron–lattice coupling can spontaneously drive significant structural rearrangements, even in mechanically robust extended π-systems.

conformation↗
DOE OSTI2020

Seasonal Dependent Impact of Ice Cloud Longwave Scattering on the Polar Climate

Most climate models neglect cloud longwave (LW) scattering because scattering is considered negligible compared to strong LW absorption by clouds and greenhouse gases. While this rationale is valid for simulating extrapolar regions, it is questionable for the polar regions, where the atmosphere is dry and hence has weak absorption, and ice clouds that have strong scattering capability frequently occur. Using the slab-ocean Community Earth System Model, we show that ice cloud LW scattering can warm winter surface air temperature by 0.8–1.8 K in the Arctic and 1.3–1.9 K in the Antarctic, while this warming becomes much weaker in polar summer. Such scattering effect cannot be correctly assessed when sea surface temperature and sea ice are prescribed as this effect is manifested through a surface-atmosphere coupling. Furthermore, cloud LW scattering is a necessity for the correct simulation of polar climate and surface radiation budget, especially in the winter.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Remote Sensing of Tundra Ecosystems Using High Spectral Resolution Reflectance: Opportunities and Challenges

Abstract Observing the environment in the vast regions of Earth through remote sensing platforms provides the tools to measure ecological dynamics. The Arctic tundra biome, one of the largest inaccessible terrestrial biomes on Earth, requires remote sensing across multiple spatial and temporal scales, from towers to satellites, particularly those equipped for imaging spectroscopy (IS). We describe a rationale for using IS derived from advances in our understanding of Arctic tundra vegetation communities and their interaction with the environment. To best leverage ongoing and forthcoming IS resources, including National Aeronautics and Space Administration’s Surface Biology and Geology mission, we identify a series of opportunities and challenges based on intrinsic spectral dimensionality analysis and a review of current data and literature that illustrates the unique attributes of the Arctic tundra biome. These opportunities and challenges include thematic vegetation mapping, complicated by low‐stature plants and very fine‐scale surface composition heterogeneity; development of scalable algorithms for retrieval of canopy and leaf traits; nuanced variation in vegetation growth and composition that complicates detection of long‐term trends; and rapid phenological changes across brief growing seasons that may go undetected due to low revisit frequency or be obscured by snow cover and clouds. We recommend improvements to future field campaigns and satellite missions, advocating for research that combines multi‐scale spectroscopy, from lab studies to satellites that enable frequent and continuous long‐term monitoring, to inform statistical and biophysical approaches to model vegetation dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Comparative Analysis of Report-Back of Research Results Strategies for Personal Chemical Exposure Data

Background. Report-back of research results (RBRR) is ethically supported and highly requested by participants yet lacks broadly transferable guidelines for RBRR. Effective RBRR must be responsive to target audience needs and may not be addressed by a ‘one-size-fits-all’ approach. Objective. Within a subset of our 19 studies on RBRR, we had the unique opportunity to carry out a comparative analysis of RBRR strategies across cohorts with similar development and evaluation methods, yet distinct in life stage, geography, number and type of chemicals assessed, and community contexts. Methods. We highlight key outcomes from three environmental health studies: an ongoing New York, NY cohort (Fair Start; n=486) and a Detroit, MI cohort (CLEAR; n=34) assessing exposure to ambient urban pollution during pregnancy, and a longitudinal cohort in Houston, TX (Houston-3H) following Hurricane Harvey (n=312). Focus group and survey data were analyzed to identify lessons learned and explore how RBRR supports understanding of environmental health. Results. Commonalities emerged in RBRR development, design, organization, and data visualization, as well as in how RBRR can contribute to an understanding of health-environment connections. Differences included preferences for individual versus community level findings, as well as distinguishable contextual considerations. For pregnancy cohorts, messaging was framed with cultural sensitivity, and to avoid unintended consequences of parental guilt due to prenatal exposures. In the post-disaster Houston-3H study, participants requested additional transparency regarding sampling design and study rationale. Significance. All RBRR case studies reported chemicals without known regulatory or health guidelines, so results were contextualized within the study population. Participants across cohorts requested multi-study comparisons to better understand their results beyond their communities. While foundational RBRR elements (e.g. plain language, graphic organizers) may supersede cohort-specific differences, RBRR should be personalized to encompass perceptions of health across different life-stage, cultural, and environmental contexts.

Vogel, Taylor J.↗
DOE OSTI2022

Identification of $\mathrm{IOMA}$-class neutralizing antibodies targeting the $\mathrm{CD4}$-binding site on the $\mathrm{HIV}$-1 envelope glycoprotein

A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope glycoprotein is of interest because, unlike the better-known VH1-2-derived VRC01-class bNAbs, it does not require a rare short light chain complementarity-determining region 3 (CDRL3). Here, we describe three IOMA-class NAbs, ACS101-103, with up to 37% breadth, that share many characteristics with IOMA, including an average-length CDRL3. Cryo-electron microscopy revealed that ACS101 shares interactions with those observed with other VH1-2 and VH1-46-class bNAbs, but exhibits a unique binding mode to residues in loop D. Analysis of longitudinal sequences from the patient suggests that a transmitter/founder-virus lacking the N276 glycan might have initiated the development of these NAbs. Together these data strengthen the rationale for germline-targeting vaccination strategies to induce IOMA-class bNAbs and provide a wealth of sequence and structural information to support such strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural basis for $\mathrm{APE1}$ processing $\mathrm{DNA}$ damage in the nucleosome

Genomic DNA is continually exposed to endogenous and exogenous factors that promote DNA damage. Eukaryotic genomic DNA is packaged into nucleosomes, which present a barrier to accessing and effectively repairing DNA damage. The mechanisms by which DNA repair proteins overcome this barrier to repair DNA damage in the nucleosome and protect genomic stability is unknown. Here, we determine how the base excision repair (BER) endonuclease AP-endonuclease 1 (APE1) recognizes and cleaves DNA damage in the nucleosome. Kinetic assays determine that APE1 cleaves solvent-exposed AP sites in the nucleosome with 3-6 orders of magnitude higher efficiency than occluded AP sites. A cryo-electron microscopy structure of APE1 bound to a nucleosome containing a solvent-exposed AP site reveal that APE1 uses a DNA sculpting mechanism for AP site recognition, where APE1 bends the nucleosomal DNA to access the AP site. Notably, additional biochemical and structural characterization of occluded AP sites identify contacts between the nucleosomal DNA and histone octamer that prevent efficient processing of the AP site by APE1. These findings provide a rationale for the position-dependent activity of BER proteins in the nucleosome and suggests the ability of BER proteins to sculpt nucleosomal DNA drives efficient BER in chromatin.

59 BASIC BIOLOGICAL SCIENCES↗