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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Formation of Linear Plasmonic Heterotrimers Using Nanoparticle Docking to DNA Origami Cages

The fabrication of complex assemblies with interesting collective properties from plasmonic nanoparticles (NPs) is often challenging. While DNA-directed self-assembly has emerged as one of the most promising approaches to forming such complex assemblies, the resulting structures tend to have large variability in gap sizes and shapes, as the DNA strands used to organize these particles are flexible, and the polydispersity of the NPs leads to variability in these critical structural features. Here, we use a new strategy termed docking to DNA origami cages (D-DOC) to organize spherical NPs into a linear heterotrimer with a precisely defined geometrical arrangement. Instead of binding NPs to the exterior of the DNA templates, D-DOC binds the NPs to either the interior or the opening of a 3D cage, which significantly reduces the variability of critical structural features by incorporating multiple diametrically arranged capture strands to tether NPs. Additionally, such a spatial arrangement of the capture strand can work synergistically with shape complementarity to achieve tighter confinement. To assemble NPs via D-DOC, we developed a multistep assembly process that first encapsulates an NP inside a cage and then binds two other NPs to the openings. Microscopic characterization shows low variability in the bond angles and gap sizes. Both UV–vis absorption and surface-enhanced Raman scattering (SERS) measurements showed strong plasmonic coupling that aligned with predictions by electrodynamic simulations, further confirming the precision of the assembly. These results suggest D-DOC could open new opportunities in biomolecular sensing, SERS and fluorescence spectroscopies, and energy harvesting through the self-assembly of NPs into more complex 3D assemblies.

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

Bridging adsorption behavior of confined CH 4 -CO 2 binary mixtures across scales

An accurate understanding of the competitive adsorption of CH 4 -CO 2 binary mixtures in nano-confined systems is critical for engineering CO 2 storage in shale gas reservoirs. Due to difficulties in making reliable experimental observations in nano-scale, atomistic simulations (ASs), such as the Grand Canonical Monte Carlo (GCMC) method, provide a viable approach to studying the adsorption behavior of confined fluids. ASs are, however, limited in the size of the compositional domain due to the high computational cost. This work proposes a framework that combines AS and the lattice Boltzmann (LB) method to bridge the physics of confined fluids across scales. The Peng–Robinson equation of state (PR-EoS) produces fugacity coefficients, which serve as input for conducting multi-component GCMC simulations. These GCMC simulations explore the competitive adsorption behavior of CH 4 -CO 2 in nano-slits at various composition, pressure, and channel-width conditions. Both components generate adsorption layers with high densities near the walls with CO 2 preferentially adsorbing compared to CH 4 on the organic walls of carbon sheets. At the mesoscale, a pseudopotential model represents the intermolecular forces in multi-component, multiple-relaxation-time LB simulations. The LB simulations are in good agreement with the GCMC results, allowing us to obtain values for tunable LB parameters. We then extend the use of LB to simulate adsorption behavior in complex networks with nano-sized channels. The phase behavior and fluid properties in the complex geometries of nano-channels differ from nano-slits and bulk systems. Furthermore, the bridging of physics from GCMC (microscale) to LB (mesoscale) via the macroscale PR-EoS connects the adsorption behavior of binary systems across scales.

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

Stabilization of Miscible Aqueous Phases via Diffusion‐Controlled Multifunctional Nanoparticle‐Ligand Complexation

Liquid‐in‐liquid structuring by harnessing miscible aqueous domains can be achieved by inducing thermodynamically defined phase separation using aqueous solutions of incompatible solutes, where immiscibility is dictated by the concentrations of the solutes. For instance, in aqueous two‐phase systems (ATPSs), the interfacial tension between the two different aqueous solutions is so small that it stabilizes the phase‐separated domains, but not their shape, thus falling short of designing tunable, robust structures. Here, we introduce a diffusion‐controlled strategy that enables liquid‐in‐liquid compartmentalization absent a thermodynamically defined interface or bulk liquid‐liquid phase separation using a barrier formed in situ at the initial contact boundary of an aqueous dispersion of multifunctional nanoparticles and a solution of multifunctional ligands in pure water or a water/alcohol mixture. The nanoparticles and ligands are entropically driven to disperse uniformly but interact at the initial contact boundary more rapidly than bulk mixing, forming a layer that establishes a barrier akin to a semi‐permeable membrane and allows the formation of tubular compartments. A wealth of opportunities is enabled by the proposed technique, where examples in separations, soft electronic devices, and ultralight porous electromagnetic shielding materials are shown.

cryogels↗
DOE OSTI2020

Ion Solvation Engineering: How to Manipulate the Multiplicity of the Coordination Environment of Multivalent Ions

During free energy analysis of solvation structures of free divalent cations, their ion pairs, and neutral aggregates in low dielectric solvents reveals the multiplicity of thermodynamically stable cation solvation configurations and identifies the micro- and macroscopic factors responsible for this phenomenon. Specifically, we show the role of ion-solvent interactions and solvent mixtures in determining the cation solvation free energy landscapes. We show that it is the entropic contribution of solvent degrees of freedom that is responsible for the solvation multiplicity, and the mutual balance between enthalpic and entropic forces or their concerted contributions is what ultimately defines the most stable ion solvation configuration and creates new ones. We show general consequences of ion solvation multiplicity on thermodynamics of complex electrolytes, specifically in the context of homogeneous or interfacial charge transfer. Identified factors and their interplay provide a pathway to formulation of solvation design rules that can be used to control bulk solvation, interfacial chemistry, and charge transfer. Our findings also suggest experimentally testable predictions.

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

Accessing Transient Isomers in the Photoreaction of Metastable‐State Photoacid

The photoreaction of a metastable‐state photoacid (mPAH) generally involves multiple isomers with various connected pathways of photoinduced structural changes during a single reaction cycle. However, only a limited number of isomers have been identified experimentally so far owing to the inherent complexity in combination with the presence of various competing electronic and vibrational processes, as well as the constantly varying interactions between mPAH isomers and solvent molecules. Here, in this work, an optical spectroscopic study on a benzimidazole‐based mPAH, a novel photoacid using benzimidazole as the structural moiety with the active proton, is reported. Through measurements of linear absorption and steady‐state fluorescence in neat solvents and binary mixtures, a pronounced effect of neat water and its binary mixture with glycerol is discovered on the photoreaction of this benzimidazole‐mPAH, manifested by the remarkably distinct spectral responses to irradiation from that observed for an organic solution under identical conditions. Measurements of time‐ and frequency‐resolved fluorescence emission further enable to access transient isomers and the associated spectral characteristics from other competing electronic excited‐state relaxation processes. Spectral deconvolution analysis and time‐dependent density functional theory calculations are applied to separate distinct spectral components and access their potential origin.

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

Cylindricity Sensitivity Thermal Model of the AGR-5/6/7 Experiment in the Advanced Test Reactor

The AGR-5/6/7 experiment is currently being irradiated in the Advanced Test Reactor (ATR) at the Idaho National Laboratory and is approximately 70% complete. Several fuel and material irradiation experiments have been planned for the U.S. Department of Energy Advanced Gas Reactor Fuel Development and Qualification Program, which supports the development and qualification of tristructural isotropic (TRISO) coated particle fuel for use in high-temperature gas-cooled reactors. The goals of these experiments are to provide irradiation performance data to support fuel process development, qualify fuel for normal operating conditions, support development of fuel performance models and codes, and provide irradiated fuel and materials for post-irradiation examination and safety testing. Originally planned and named as separate fuel experiments, but subsequently combined into a single test train, AGR-5/6/7 is testing low-enriched uranium oxycarbide TRISO fuel. The AGR-5/6/7 test train has 5 capsules with thermocouples and independent gas control mixtures. Unique to this paper is a sensitivity study concerning the cylindricity of the graphite holders containing the fuel compacts and their eccentricity in relation to the stainless-steel capsule walls. Each capsule has small nubs on the outside used for centering the graphite holder inside the stainless-steel capsule with a small gas gap used to control temperature. Due to machining tolerances of these nubs and vibration wearing the nubs down when the experiment is running in the reactor, the possibility exists that the holder may move around radially. Each capsule is equipped with several thermocouples placed at various radii and depths within each graphite holder. This paper will show the sensitivity of offsetting the graphite holder for various radii in 45-degree increments around the circle with the objective of minimizing the difference between the measured thermocouples and the modeled thermocouple temperatures. Separate gas mixtures of helium/neon are introduced into this gas gap between the holder and capsule wall and changed as necessary to maintain the desired thermocouple temperatures to keep the fuel compacts at constant temperature as the nuclear reactor conditions change. The goal of the sensitivity study is to find a radius and an angle to offset the holder from perfectly centered for each of the five capsules separately. The complex thermal model includes fission heating, gamma heating, radiation heat transfer, and heat transfer via conduction and radiation across the control gaps. Subroutines linked to the thermal model offer an easy method to offset the graphite holder from the capsule walls without remeshing the entire model.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

A Comprehensive Investigation into the Effect of a Low Surface Energy Treatment on Gas Hydrate, Asphaltene, and Wax Formation, Deposition, and Adhesion

The formation/precipitation and deposition of pipeline solids, such as gas hydrates, asphaltenes, and waxes have long plagued production fields. Given the vast differences in chemistries of these solids, any current prevention or mitigation strategy, particularly for cases in which multiple issues are a concern, is likely to involve an extensive assortment of chemical additives that are both costly and add complexity to the system. Surface treatments (coatings), on the other hand, present a relatively viable option for management strategies. A chemically and physically robust surface treatment with the ability to address deposition issues for multiple pipeline solids could not only decrease the operating expenditures for a field through material cost savings and obviation of downstream separation, but could also simplify produced fluids by eliminating additional chemicals from the mixture. The purpose of this study was to explore the feasibility of a particular surface treatment as part of a solids management strategy. This work used an omniphobic surface treatment to probe its effects on gas hydrate, asphaltene, and wax deposition. Specifically, an interfacial tensiometer (IFT) collected contact angle measurements for wettability studies. High-pressure rocking cells studied gas hydrate nucleation and deposition. A bench-scale flow loop quantified the deposition of oil and asphaltenes after a set time period. Finally, a mechanical shear device measured the adhesion force of wax deposits on untreated/treated surfaces. Static contact angle results showed that the omniphobic surface treatment had reduced surface interaction with water droplets in air, altering from the complete wetting on corroded surfaces to slightly hydrophobic conditions of greater than 100°. In addition, rocking-cell tests indicated that these omniphobic surface treatments may prevent gas hydrate deposition for up to 72 hours. The gas hydrate rocking-cell tests also demonstrated possible increases in induction time and occasional elimination of hydrate nucleation with the surface treatment. Finally, the surface treatment application, which also decreased surface roughness, showed that crude oil and asphaltene particles deposition, as well as the shear required to remove solidified wax deposits, could be reduced by a large factor. Overall, promising results were recorded for all major flow-assurance solids in the presence of the surface treatment.

Engineering↗
DOE OSTI2023

Site Disorder as a Predictor for Compositionally Complex 5RE 2 Zr 2 O 7 Ceramic Phase Stability

Here, phase formation and stability of five component compositionally complex rare earth zirconates (5RE 2 Zr 2 O 7 ) were investigated by X-ray diffraction and electron microprobe analysis. Zirconates with different rare earth compositions (LaNdSmEuDy, LaNdSmEuYb, LaNdEuErYb, LaNdDyErYb, SmEuDyYHo, LaYHoErYb, and DyYHoErYb) were synthesized at 1700°C and 2000°C by the solid-state method to investigate the effect of A-site site disorder (δ A ) on phase stability. Increased site disorder results from mixed cation occupancy with localized crystallographic strain and bond disorder. Compositions LaNdSmEuDy (δ A = 4.6) and LaNdSmEuYb (δ A = 6.0) produced a single pyrochlore phase and compositions SmDyYHoErYb (δ A = 2.8), LaYHoErYb (δ A = 6.2), and DyYHoErYb (δ A = 1.7) produced a single fluorite phase. High δ A compositions LaNdEuErYb (δ A = 6.9) and LaNdDyErYb (δ A = 7.2) produced a pyrochlore and fluorite phase mixture at 1700°C. Single phase was obtained for the latter composition at 2000°C. Of the single phase compositions calcined at 1700°C, LaNdSmEuYb and LaYHoErYb (both with largest δ A ) showed decomposition to mixed fluorite and pyrochlore phases during lower temperature anneals, indicating entropic stabilization. Comparison with prior work shows a temperature dependence of the critical δ A for phase stability, and compositions near it are expected to be entropy stabilized.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Evaluation of a Robust, In-Situ Surface Treatment for Pipeline Solids Deposition Mitigation in Flowing Systems

Abstract The formation/precipitation and deposition of pipeline solids, such as gas hydrates, asphaltenes, and waxes have long plagued production fields. Given the vast differences in chemistries of these solids, any current prevention or mitigation strategy, particularly for cases where multiple issues are a concern, is likely to involve an extensive assortment of undefined chemical additives that are both costly and add complexity to the system. Surface treatments (coatings), on the other hand, present a relatively new viable option for management strategies. A chemically and physically robust surface treatment with the ability to address deposition issues for multiple pipeline solids could not only decrease the operating expenditures for a field through material cost savings and obviation of downstream separation, but could also simplify produced fluids by eliminating additional chemicals from the mixture. The purpose of this study is to explore the feasibility of a particular surface treatment as part of a solids management strategy. This work utilizes an omniphobic surface treatment to probe its effects on gas hydrate, asphaltene, and wax deposition. Specifically, high pressure rocking cells are employed to study gas hydrate nucleation and deposition. A bench-scale flowloop filled with crude oil and heptane is used to quantify the deposition of crude oil and asphaltenes after a set time period. Lastly, a mechanical shear device measures the adhesion force of wax deposits on untreated/treated surfaces. The gas hydrate rocking cell tests demonstrate an increase in induction time and occasional elimination of hydrate nucleation with the surface treatment. Moreover, the same apparatus indicates that the critical shear to avoid hydrate deposition may be lowered in the presence of the surface treatment compared to untreated pristine carbon steel coupons. A custom-built asphaltene flowloop then establishes that this surface treatment is effective in dramatically reducing the deposition of the aliphatic components of a crude oil, with a moderate reduction in the asphaltene fraction. Finally, mechanical adhesion force measurements for solidified paraffin wax display trends in agreement with the asphaltene results. The surface treatment on both pristine and corroded surfaces is able to reduce the adhesion of wax deposits to values below a pristine, untreated surface.

03 NATURAL GAS↗
DOE OSTI2025

Stable single-site organonickel catalyst preferentially hydrogenolyses branched polyolefin C–C bonds

Current methods of processing accumulated polyolefin waste typically require harsh conditions, precious metals or high metal loadings to achieve appreciable activities. Here, in this work, we examined supported, single-site organonickel catalysts for polyolefin upcycling. Chemisorption of Ni(COD) 2 (COD, 1,5-cyclooctadiene) onto Brønsted acidic sulfated alumina (AlS) yields a highly electrophilic Ni(I) precatalyst, AlS/Ni(COD) 2 , which is converted under H 2 to the active AlS/Ni II H catalyst. This single-site system exhibits unique hydrogenolysis selectivity that favours cleaving branched polyolefin C–C linkages, enabling the hydrogenolytic separation of polyethylene and isotactic polypropylene (iPP) mixtures. Moreover, AlS/Ni II H remains highly selective and active for hydrogenolysis of iPP admixed with polyvinyl chloride, and the spent catalyst can be repeatedly regenerated by AlEt3 treatment. Experimental mechanistic analysis and density functional theory modelling reveal a turnover-limiting C–C scission pathway featuring β-alkyl transfer and strong olefin binding. These results highlight the potential of nickel-based systems for the selective upcycling of complex plastic waste streams.

green chemistry↗
DOE OSTI2021

Visualization of Jet Impingement and Ignition in a Piston-Cylinder Chamber

The transportation sector accounts for almost a third of the United States' energy consumption. We are developing predictive simulations of the complex in-cylinder processes of internal combustion engines to improve performance and decrease pollutant emissions. We provide a first look at the jet impingement and ignition inside a piston-cylinder chamber using volume rendering. Through the visualization, we constructed a complete 3D picture of the jet impingement on the piston-bowl walls leading to the formation of pockets of auto-ignition of the fuel-air mixture. These auto-ignition pockets subsequently lead to flame stabilization, releasing the chemical energy for conversion to useful work. A detailed physical picture of flame stabilization, as provided by the visualization techniques presented in this study, help in the design of next-generation internal combustion engines.

91 SC - Advanced Scientific Computing Reseach (ASC↗
DOE OSTI2025

Conformational Change in a Four‐Tetrad DNA G‐Quadruplex upon Intercalation of a Small‐Molecule Ligand PyDH2

Abstract G‐quadruplexes (G4s) are non‐canonical DNA structures implicated in a number of biological processes. Small‐molecule ligands can alter stability and folding of G4s, which can potentially be exploited for therapeutic purposes. In this work, we investigate the interaction of telomeric DNA fragment fromTetrahymena thermophila(TET25, 5′‐G(TTGGGG) 4‐ 3′) with a G4 ligand PyDH2 belonging to the bisquinolinium family. When alone, TET25 adopts a mixture of three conformations, with the most abundant being a four‐tetrad hybrid G4. In the presence of PyDH2, surprisingly, TET25 folds into an antiparallel chair G4, with PyDH2 intercalated between G‐tetrads 2 and 3, according to our crystal structure. The structure represents the second example, and the first crystallographic evidence, of ligand intercalation into a G4. In solution, the interaction of PyDH2 and TET25 leads to a number of complexes differing by G4 topology and binding stoichiometry, strong stabilization of G4 (∆T m = 12.4 °C in the presence of one equiv. of PyDH2) and large hysteresis of ∼10 °C, suggesting that ligand binding and G4 folding processes are complex.

Chemistry↗
DOE OSTI2021

Selective Biosorption of Valuable Rare Earth Elements Among Co-Occurring Lanthanides

To meet the increasing demand for rare earth elements (REEs) essential for low carbon-intensity energy technologies, new methods are needed for selective REE extraction from unconventional resources. Only a few REEs have significant economic value, but isolation of target rare earths from co-occurring lanthanides is challenging due to their similar chemical behavior. We present a novel approach to enhance separation of specific REEs from lanthanide mixtures. Escherichia coli cells engineered with lanthanide binding tags (LBTs) were immobilized in nonadsorbing, permeable polyethylene glycol diacrylate beads and packed into continuous flow, fixed-bed columns. Breakthrough of 15 rare earths in the +3 oxidation state resulted in notable differences in adsorption selectivity, with greatest separation between europium (Eu) and lanthanum (La) due to competitive displacement. REE adsorption onto fixed-bed columns was predicted by coupling a surface complexation model to a calibrated one-dimensional dual porosity transport model that accounts for interbead advective and intrabead diffusive transport. A tradeoff between high-abundance, low-affinity native carboxyl sites and low-abundance, high-affinity engineered LBT sites dictates process recovery efficiency and selectivity. Key chemical and operational parameters are identified to maximize selective extraction of high-value lanthanides, achieving a threefold enhancement of Eu recovery relative to La in a mixed REE solution.

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

Temperature and anion ligand field dependence of LnCl 3 (Ln = Nd, Dy, Sm) electronic absorption spectra in LiCl–KCl eutectic molten salt

A comprehensive knowledge of the coordination, bonding, and speciation of elements in molten salt mixtures is necessary to understand and predict the chemical and physical properties of the salt. Absorption spectroscopy can yield information about the chemistry of species of interest in alkali halide molten salt mixtures by revealing information about the electronic structure and transitions of those species. In this study, ultraviolet (UV), visible (vis), and near-infrared (NIR) absorption spectroscopy was used to examine changes to the electronic structure of trivalent Nd, Sm, and Dy in LiCl–KCl eutectic molten salt with changes in temperature and the anion composition of the melt. With increasing temperature, changes to spectral features suggest a distortion of the coordination complexes. Changes to lineshape with the substitution of alternative halide anions were examined and analyzed, revealing differences in the coordination for I – versus F – with the lanthanides. Gaussian peak fitting was used to show that the changes in lineshape with the progressive addition of F – anions can be explained by the superposition of a set of absorption bands from complexes with all Cl – anion ligands and a set of blueshifted absorption bands from complexes containing both F – and Cl – anion ligands. Finally, this work yields a new method to analyze and interpret change to electronic absorption spectra for f-block elements dissolved in alkali halide molten salts as well as new observations of the interactions of larger and smaller halide anions with lanthanides in Cl – -based molten salts.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Heterogenization of Homogeneous Ruthenium(II) Catalysts for Carbon-Neutral Dehydrogenation of Polyalcohols

Liquid organic hydrogen carrier (LOHC) systems are an excellent alternative to pressurized gas and liquid hydrogen storage technologies due to their high volumetric storage capacities and straightforward adaptation to existing infrastructure. Homogeneous catalysts are promising for the selective and reversible release of hydrogen from LOHC. However, separation from product mixtures and recycling inhibit their use, particularly when comprised of costly low-abundance elements, motivating the development of heterogeneous versions that are more easily recovered and reused. Here, we describe two methods for the heterogenization of molecular Ru catalysts that efficiently dehydrogenate the polyalcohol LOHCs ethylene glycol (EG) and 1,2-propanediol (1,2-PDO). The heterogeneous versions of these catalysts maintain catalytic activity for hydrogen production comparable to the homogeneous complexes, with up to 81% conversion and 99% selectivity. Further, DFT modeling indicates mechanistic similarities for the dehydrogenations of EG and 1,2-PDO, with the rate-limiting steps associated with protonation of the Ru–H bond to form H 2 and the alkoxide species coordinated to Ru(II), followed by β-hydride elimination to regenerate the Ru–H bond. Overall, the data suggest these heterogenized molecular catalysts have potential for practical use in polyalcohol-based LOHC systems.

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

Exchange-Mediated Transport in Battery Electrolytes: Ultrafast or Ultraslow?

Understanding the mechanisms of charge transport in batteries is important for the rational design of new electrolyte formulations. Persistent questions about ion transport mechanisms in battery electrolytes are often framed in terms of vehicular diffusion by persistent ion–solvent complexes versus structural diffusion through the breaking and reformation of ion–solvent contacts, i.e., solvent exchange events. Ultrafast two-dimensional (2D) IR spectroscopy can probe exchange processes directly via the evolution of the cross-peaks on picosecond time scales. However, vibrational energy transfer in the absence of solvent exchange gives rise to the same spectral signatures, hiding the desired processes. Here we employ 2D IR on solvent resonances of a mixture of acetonitrile isotopologues to differentiate chemical exchange and energy-transfer dynamics in a comprehensive series of Li + , Mg 2+ , Zn 2+ , Ca 2+ , and Ba 2+ bis(trifluoromethylsulfonyl)imide electrolytes from the dilute to the superconcentrated regime. No exchange phenomena occur within at least 100 ps, regardless of the ion identity, salt concentration, and presence of water. All of the observed spectral dynamics originate from the intermolecular energy transfer. These results place the lower experimental boundary on the ion–solvent residence times to several hundred picoseconds, much slower than previously suggested. With the help of MD simulations and conductivity measurements on the Li + and Zn 2+ systems, we discuss these results as a continuum of vehicular and structural modalities that vary with concentration and emphasize the importance of collective electrolyte motions to ion transport. These results hold broadly applicable to many battery-relevant ions and solvents.

25 ENERGY STORAGE↗
DOE OSTI2021

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial enzyme that degrades β-lactam antibiotics. We present structure-guided computational methods for designing peptide macrocycles built from mixtures of l - and d -amino acids that are able to bind to and inhibit targets of therapeutic interest. Our methods explicitly consider the propensity of a peptide to favor a binding-competent conformation, which we found to predict rank order of experimentally observed IC 50 values across seven designed NDM-1- inhibiting peptides. We were able to determine X-ray crystal structures of three of the designed inhibitors in complex with NDM-1, and in all three the conformation of the peptide is very close to the computationally designed model. In two of the three structures, the binding mode with NDM-1 is also very similar to the design model, while in the third, we observed an alternative binding mode likely arising from internal symmetry in the shape of the design combined with flexibility of the target. Although challenges remain in robustly predicting target backbone changes, binding mode, and the effects of mutations on binding affinity, our methods for designing ordered, binding-competent macrocycles should have broad applicability to a wide range of therapeutic targets.

42 ENGINEERING↗