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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

PDG: A Composite Method Based on the Resolution of the Identity

The Gaussian-3 (G3) composite approach for thermochemical properties is revisited in light of the enhanced computational efficiency and reduced memory costs by applying the resolution-of-the-identity (RI) approximation for two-electron repulsion integrals (ERIs) to the computationally demanding component methods in the G3 model: the energy and gradient computations via the second-order Møller–Plesset perturbation theory (MP2) and the energy computations using the coupled-cluster singles–doubles method augmented with noniterative triples corrections [CCSD(T)]. Efficient implementation of the RI-based methods is achieved by employing a hybrid distributed/shared memory model based on MPI and OpenMP. The new variant of the G3 composite approach based on the RI approximation is termed the RI-G3 scheme, or alternatively the PDG method. The accuracy of the new RI-G3/PDG scheme is compared to the “standard” G3 composite approach that employs the memory-expensive four-center ERIs in the MP2 and CCSD(T) calculations. Taking the computation of the heats of formation of the closed-shell molecules in the G3/99 test set as a test case, it is demonstrated that the RI approximation introduces negligible changes to the mean absolute errors relative to the standard G3 model (less than 0.1 kcal/mol), while the standard deviations remain unaltered. Furthermore, the efficiency and memory requirements for the RI-MP2 and RI-CCSD(T) methods are compared to the standard MP2 and CCSD(T) approaches, respectively. The hybrid MPI/OpenMP-based RI-MP2 energy plus gradient computation is found to attain a 7.5× speedup over the standard MP2 calculations. For the most demanding CCSD(T) calculations, the application of the RI approximation is found to nearly halve the memory demand, confer about a 4–5× speedup for the CCSD iterations, and reduce the computational time for the compute-intensive triples correction step by several hours.

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

The Role of Spin–Orbit Coupling in the Linear Absorption Spectrum and Intersystem Crossing Rate Coefficients of Ruthenium Polypyridyl Dyes

The successful use of molecular dyes for solar energy conversion requires efficient charge injection, which in turn requires the formation of states with sufficiently long lifetimes (e.g., triplets). The molecular structure elements that confer this property can be found empirically, however computational predictions using ab initio electronic structure methods are invaluable to identify structure-property relations for dye sensitizers. The primary challenge for simulations to elucidate the electronic and nuclear origins of these properties is a spin-orbit interaction which drives transitions between electronic states. Here, in this work, we present a computational analysis of the spin-orbit corrected linear absorption cross sections and intersystem crossing rate coefficients for a derivative set of phosphonated tris(2,2'-bipyridine)ruthenium(2+) dye molecules. After sampling the ground state vibrational distributions, the predicted linear absorption cross sections indicate that the mixture between singlet and triplet states plays a crucial role in defining the line shape of the metal-to-ligand charge transfer bands in these derivatives. Additionally, an analysis of the intersystem crossing rate coefficients suggests that transitions from the singlet into the triplet manifolds are ultrafast with rate coefficients on the order of 10 13 s -1 for each dye molecule.

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

Characterizing Surface Ice-Philicity Using Molecular Simulations and Enhanced Sampling

The formation of ice, which plays an important role in diverse contexts ranging from cryopreservation to atmospheric science, is often mediated by solid surfaces. Although surfaces that interact favorably with ice (relative to liquid water) can facilitate ice formation by lowering nucleation barriers, the molecular characteristics that confer ice-philicity to a surface are complex and incompletely understood. To address this challenge, here we introduce a robust and computationally efficient method for characterizing surface ice-philicity that combines molecular simulations and enhanced sampling techniques to quantify the free energetic cost of increasing surface–ice contact at the expense of surface–water contact. Using this method to characterize the ice-philicity of a family of model surfaces that are lattice matched with ice but vary in their polarity, we find that the nonpolar surfaces are moderately ice-phobic, whereas the polar surfaces are highly ice-philic. In contrast, for surfaces that display no complementarity to the ice lattice, we find that ice-philicity is independent of surface polarity and that both nonpolar and polar surfaces are moderately ice-phobic. Furthermore, our work thus provides a prescription for quantitatively characterizing surface ice-philicity and sheds light on how ice-philicity is influenced by lattice matching and polarity.

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

Nanocomposites Based on Coil-Comb Diblock Copolymers

The polymer chain architecture is an important factor determining the phase behavior of nanoparticle (NP) assembly in polymer matrices. Block copolymers (BCPs) containing a random copolymer (RCP) block present a convenient variation on traditional BCPs to tune the interaction parameters between the polymer blocks and the nanofillers as well as to evaluate the effect of the chain architecture on the NP arrangements within BCP microdomains. Here, we synthesized BCPs with a coil polystyrene (PS) block and a comb RCP block through reversible addition-fragmentation chain transfer polymerization. The RCP block consists of methyl- and lauryl acrylates, the latter of which confers a long-chain alkyl moiety to favorably interact with alkyl-passivated NPs. BCPs showing lamellar, cylindrical, and mixed morphologies were obtained by varying the volume fractions of the RCP block (f RCP ). In comparison to coil-coil BCP, the coil-comb BCPs show highly asymmetric phase behavior with respect to fRCP, where lamellar morphologies were observed at fRCP from 0.31 to 0.51. NPs in the size of 4-5 nm were successfully incorporated in the RCP block of the BCPs with periodicities of 30-60 nm. An order-to-order phase transition from lamellae to PS cylinders was observed after the addition of only 1-2 vol % 5 nm NPs into the BCP with a periodicity of 25 nm and f RCP of 0.51. Self-consistent field theory-density functional theory simulations qualitatively described the observed morphologies and phase transitions in the nanocomposites. Here, the current study presents a platform to fabricate nanocomposites with NP assemblies in coil-comb BCPs that contain a random copolymer block and provides insight into how polymer chain architectures can affect the phase behavior of BCPs and nanocomposites.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Gold-Nanocluster-Mediated Delivery of siRNA to Intact Plant Cells for Efficient Gene Knockdown

RNA interference, which involves the delivery of small interfering RNA (siRNA), has been used to validate target genes, to understand and control cellular metabolic pathways, and to use as a "green" alternative to confer pest tolerance in crops. Conventional siRNA delivery methods such as viruses and Agrobacterium -mediated delivery exhibit plant species range limitations and uncontrolled DNA integration into the plant genome. Here, we synthesize polyethylenimine-functionalized gold nanoclusters (PEI-AuNCs) to mediate siRNA delivery into intact plants and show that these nanoclusters enable efficient gene knockdown. We further demonstrate that PEI-AuNCs protect siRNA from RNase degradation while the complex is small enough to bypass the plant cell wall. Consequently, AuNCs enable gene knockdown with efficiencies of up 76.5 ± 5.9% and 76.1 ± 9.5% for GFP and ROQ1, respectively, with no observable toxicity. Our data suggest that AuNCs can deliver siRNA into intact plant cells for broad applications in plant biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Robust, High-Performing Maize–Perovskite-Based Solar Cells with Improved Stability

Herein, we focus on improving the long-term chemical and thermomechan-ical stability of perovskite solar cells (PSCs), two major challenges currently limiting their commercial deployment. Our strategy incorporates a long-chain starch polymer into the perovskite precursor. The starch polymer confers multiple beneficial effects by forming hydrogen bonds with the methylammonium iodide precursor, templating perovskite growth that results in a compact and homogeneous film deposited in a simple one-step coating (antisolvent-free). The inclusion of starch in the methylammonium lead iodide films strongly improves their thermomechanical and environmental stability while maintaining a high photovoltaic performance. The fracture energy (G c ) of the film is increased to above 5 J/m 2 by creating a nanocomposite that provides intrinsic reinforcement at grain boundaries. Additionally, improved optoelectronic properties achieved with the starch polymer enable good photostability of the active layer and enhanced resistance to thermal cycling.

14 SOLAR ENERGY↗
DOE OSTI2026

Elucidating the Structural and Electronic Effects of Ni and Mn Cationic Incorporation on CoOOH for Efficient Benzyl Alcohol Electrooxidation

Transition-metal oxyhydroxides such as CoOOH are promising low-cost electrocatalysts for the selective electrooxidation of organic molecules, yet the influence of ubiquitous transition-metal impurities on their performance and durability remains poorly understood. Here, we experimentally probed the individual and synergistic electrochemical and structural effects of Ni and Mn incorporations into model CoOOH electrocatalysts toward an efficient benzyl alcohol oxidation reaction (BAOR). Comprehensive electrochemical, microscopic, and spectroscopic analyses reveal that Ni incorporation enhances charge-transfer kinetics and overall activity through the formation of catalytically active Ni 3+ sites, whereas Mn exhibited a more complex but interesting role. At the early stages of operation, Mn 4+ acts as a stabilizing surface layer that mitigates catalyst degradation but partially blocks Co sites before they undergo gradual leaching. The concurrent incorporation of both Ni and Mn yields a trimetallic 2NMC@NF electrocatalyst that integrates the activity benefits of Ni with the stability conferred by Mn, achieving 92.9% benzyl alcohol conversion and 91.4% Faradaic efficiency after 24 h at 1.5 V vs RHE. These findings elucidate how trace Ni and Mn impurities, often introduced from electrolytes or external sources, can modulate the lattice and electronic structure of CoOOH, offering a design strategy for enhancing both activity and long-term stability in electrocatalytic organic oxidation.

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

Hydrophobic Molecule Monolayer Brush-Tethered Zinc Anodes for Aqueous Zinc Batteries

Aqueous zinc batteries are of great interest as a rechargeable energy storage system, particularly owing to the low cost and high safety of aqueous electrolytes, as well as the high capacity of zinc anodes. Unfortunately, the wide commercialization of aqueous zinc batteries is impeded by the irreversible water reduction and irregular zinc evolution issues on the anode side. Hereby, a hydrophobic and ultrathin polystyrene molecule brush layer is tethered onto the surface of zinc metal anodes to tackle the above limitations. Here, experimental investigations reveal that the waterproof artificial layer can sustain fast interfacial ionic transportation, minimize hydrogen evolution, and smoothen Zn deposition, thus conferring enhanced electrochemical performance to the as-protected Zn anode in both symmetric Zn//Zn cells and Zn//LiV 3 O 8 full cells.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Combining Sub-nanometer Adhesion and Capping Layers for Thermally Stable Nanometer-Thick Au Films

Improving the thermal stability of Au thin films is critical if thermo-plasmonic applications such as heat-assisted magnetic recording are to become commercially viable. In this work, Al capping layers are deposited on M/Au films, where adhesion metal M = Ti or Ta, and are investigated for their utility in stabilizing Au thin films against dewetting. Therefore, contrary to previous investigations, it was found that thinner capping layers (0.5 nm) result in a greater stability than that conferred by thicker (1-5 nm) layers. Deposition of 0.5 nm of Al, which subsequently oxidizes when exposed to air, resulted in up to 10x stability enhancement. Similarly, capping with 0.5 nm Al resulted in less damping of the plasmonic response than with thicker capping layers. Finally, based on this work and previous work on metallic adhesion layers, optimally stable systems for thermo-plasmonic applications are proposed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Aldol Condensation and Esterification over Ti-Substituted *BEA Zeolite: Mechanisms and Effects of Pore Hydrophobicity

Aldol condensation and esterification reactions provide paths to upgrade ethanol and acetaldehyde to higher- value molecules useful as fuels or intermediates for the synthesis of polymers. Transition-metal-substituted BEA zeolites (M-BEA) catalyze these reactions; however, the mechanisms for these processes in M-BEA and the effects of incidental or purposefully included silanol groups are not reported. Here, we combine kinetic and spectroscopic measurements obtained during catalytic reactions of acetaldehyde (CH 3 CHO), ethanol (C 2 H 5 OH), and hydrogen (H 2 ) mixtures over a series of Ti-BEA catalysts that possess a known range of silanol group densities to examine the kinetic relevance of intervening steps and the impact of silanol groups on catalytic rates. Across all Ti-BEA, rates for aldol condensation and esterification increase with the pressure of CH 3 CHO; however, C 2 H 5 OH and H 2 O weakly inhibit the rates of these reactions. The substitution of CD 3 CDO for CH 3 CHO decreases aldol condensation rates slightly (~10%) but leads to greater esterification rates (2- to 5-fold). The kinetic isotope effects together with the measured dependence of rates on reactant pressures suggest that aldol condensation and esterification occur on unoccupied Ti sites and involve multiple kinetically relevant steps. CH 3 CHO deprotonates irreversibly, and the kinetically relevant nucleophilic attack of the enolate to CH 3 CHO* (i.e., adsorbed CH 3 CHO on Ti sites) leads to aldol products, while the nucleophilic attack of the enolate to C 2 H 5 OH* gives esters. Selectivities toward aldol condensation increase with the ratio of CH 3 CHO to C 2 H 5 OH pressure and with increases in the silanol density of the as-synthesized Ti-BEA. During catalysis, in situ infrared spectroscopy demonstrates that these silanol groups react with C 2 H 5 OH to form ethoxysilane groups (i.e., SiOC 2 H 5 ) that modify the polarity of the environment near Ti active sites. As initial silanol densities increase, steady-state turnover rates for aldol condensation and esterification increase by factors of 5 and 2, respectively. The changes in rates and selectivities among Ti-BEA catalysts likely reflect changes in excess free energies of transition states for enolization and nucleophilic attack of the enolate to adsorbed coreactants. The differences in excess stability report on the interactions among reactive intermediates at framework Ti atoms and the ethoxysilane and remaining silanol groups present. Furthermore, the in situ modification of these pore environments confers changes in the stability of reactive species in a manner that contradicts intuition when considering the initial state of the catalyst but can be reconciled after accounting for the formation of persistent alkoxy surface moieties in the pores.

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

Experimental and Computational Evaluation of Nicotinamide Cofactor Biomimetics

Oxidoreductase enzymes are widely used biocatalysts due to their high enantioselectivity and broad substrate compatibility in useful transformations. Many oxidoreductases require nicotinamide cofactors (i.e., NAD(P)H). To replace this costly natural cofactor, synthetic nicotinamide cofactor biomimetics (NCBs) offer different shapes, binding affinities, and reducing potentials that exceed the capabilities of wild-type NAD(P)H. However, the ill-defined structure–activity relationships (SARs) of various NCBs slow rationally guided innovation, such as customized reducing potentials. Here, we dissect two essential elements of NCB design, holding the nicotinamide invariant. First, the linker length between the nicotinamide and an unconjugated aromatic ring uncovered unexpected benefits to redox activity for two or three carbon linkers. Second, substitution on this unconjugated aryl group (Ring 2) might not be expected to affect activity. However, SAR trends demonstrate substantial benefits to reductive potential conferred by electron-donating functionalities on Ring 2. Furthermore, catalysis by two enzymes demonstrates enzyme-dependent tolerance or sensitivity to the NCB structures. Density functional theory (DFT) and computational modeling provide a theoretical framework to understand and build upon these observations. Ring 2 reaches up to the nicotinamide to stabilize its positive charge after oxidation through π–π stacking and charge transfer. Thus, the systematic examination of NCB’s stability, electrochemical redox potentials, and kinetics uncovers trends for the improved design of NCBs.

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

Structural Analysis of 23S rRNA Methylating Enzyme Cfr Reveals RNA-Binding Determinants for Methylation Regiospecificity and Antibiotic Resistance

The 23S rRNA methylating enzyme Cfr, found in pathogens including Staphylococcus aureus, Clostridium difficile, Escherichia coli, and Klebsiella pneumoniae, confers resistance to phenicols, lincosamides, oxazolidinones (including linezolid), pleuromutilins, and streptogramins A (the PhLOPS A phenotype). Cfr catalyzes methylation of the C8 position of the A2503 base in 23S rRNA, the recognition site of the above antibiotic classes. Along with the RlmN housekeeping enzyme, Cfr can also promote methylation of the C2 position of the same base. The molecular and structural basis of Cfr’s dual substrate specificity is not known, which hinders our ability to design Cfr-targeting inhibitors necessary to curb PhLOPS A resistance. Here, we present the first crystal structure of Cfr and a detailed analysis of its possible interactions with rRNA. Using structure-guided mutagenesis, mass spectrometry analysis of in cellulo 23S rRNA methylated species, and in cellulo resistance studies, we identify the key amino acids essential for Cfr methylation and multidrug resistance activity. In particular, we found that Cfr’s Q329 residue is important for C8- specific methylation. These data provide a framework for further studies of the biochemistry, structure, and inhibition of this important resistance determinant.

AlphaFold↗
DOE OSTI2020

Biomimetic Rebuilding of Multifunctional Red Blood Cells: Modular Design Using Functional Components

The design and synthesis of artificial materials that mimic the structures, mechanical properties, and ultimately functionalities of biological cells remains a current holy grail of materials science. Here based on a silica cell bio-replication approach, we report the design and construction of synthetic rebuilt red blood cells (RRBCs) that fully mimic the broad properties of native RBCs: size, biconcave shape, deformability, oxygen carrying capacity, long circulation time. Four successive nano-scale processing steps: RBC bioreplication, layer-by-layer polymer deposition, and precision silica etching, followed by RBC ghost membrane vesicles fusion are employed for RRBC construction. A panel of physicochemical analyses including zeta potential measurement, fluorescence microscopy, and antibody-mediated agglutination assay proved the recapitulation of RBC shape, size, and membrane structure. Flow-based deformation studies carried out in a microfluidic blood capillary model confirrned the ability of RRBCs to deform and pass through small slits and reconstitute themselves in a manner comparable to native RBCs. Circulation studies of RRBCs conducted ex-ovo in a chick embryo and in vivo in a mouse model demonstrated the requirement of both deformability and native cell membrane surface to achieve long-term circulation. To confer additional non-native functionalities to RRBCs, we developed modular procedures in which to load functional cargos such as hemoglobin, drugs, magnetic nanoparticles, and ATP biosensors within the RRBC interior to enable various functions, including oxygen delivery, therapeutic drug delivery, magnetic manipulation, and toxin biosensing and detection. Taken together, RRBCs represent a class of long circulating RBC-inspired artificial hybrid materials with a broad range of potential applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Evaluating the Transport Mechanism for Lignocellulosic Inhibitors in Zymomonas mobilis

The conversion of lignocellulosic biomass to biofuels and bioproducts is limited by small inhibitory molecules generated during the pretreatment process. The diverse compounds within the cell wall hydrolysate including aldehydes, carboxylic acids, phenolics, and alcohols inhibit microbial growth by disrupting microbial membranes. Although Zymomonas mobilis combines high ethanol productivity with hopanoid-rich membranes that confer solvent tolerance, hydrolysate compounds still inhibit microbial growth. One proposed mitigation strategy is to pump these molecules out through active transport processes, reducing direct toxicity. However, if passive permeation rates are high, active transport would create a futile cycle where the exported molecules diffuse back in, creating a net drag on fitness. To investigate this hypothesis, we measure the passive permeation for thirty-three lignocellulose derived compounds using atomistic molecular dynamics simulations with enhanced sampling. Permeability coefficients determined spanned more than eight orders of magnitude driven largely by the balance between hydrophobicity and polarity. Hydrophobic inhibitors such as aromatic acids, aldehydes, and short chain alcohols readily partitioned into the membrane and showed high permeability consistent with rapid passive influx and strong toxicity. Most polar molecules have lower but still appreciable permeation rates, with only the most polar sugars having low permeabilities. By integrating these predictions together with hydrolysate composition information, we find that most of these molecules are so permeable that futile cycles where passive permeation overwhelms efflux is highly likely. These findings provide a predictive framework for strain engineering, highlighting that, for highly permeable inhibitors, reducing extracellular inhibitor concentrations through hydrolysate detoxification, pretreatment optimization, or dilution may be necessary to mitigate futile cycling and improve microbial productivity in industrial biorefineries.

Zymomonas mobilis↗
DOE OSTI2020

Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform

Advances in high-throughput synthetic biology technologies based on the CRISPR/Cas9 system have enabled a comprehensive assessment of mutations conferring desired phenotypes, as well as a better understanding of genotype-phenotype correlations in protein engineering. Engineering antibodies to enhance properties such as binding affinity and stability plays an essential role in therapeutic applications. Here we report a method, multiplex navigation of antibody structure (MINAS), that combines a CRISPR/Cas9-based trackable editing method and fluorescent-activated cell sorting (FACS) of yeast-displayed libraries. We designed mutations in all of the complementarity-determining and framework regions of a well-characterized scFv antibody and mapped the contribution of these regions to enhanced properties. We identified specific mutants that showed higher binding affinities up to 100-fold compared to the wild-type. This study expands the applicability of CRISPR/Cas9-based trackable protein engineering by combining it with a surface display platform.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

How Does Escherichia coli Allocate Proteome?

Microorganisms are shown to actively partition their intracellular resources, such as pro- teins, for growth optimization. Recent experiments have begun to reveal molecular com- ponents unpinning the partition; however, it remains unclear quantitatively how individual parts orchestrate to yield precise resource allocation that is both robust and dynamic. Here we developed a coarse-grained mathematical framework that centers on guanosine pentaphosphate (ppGpp)-mediated regulation, and used it to systematically uncover the design principles of proteome allocation in Escherichia coli. Our results showed that cellular ability of resource partition lies in an ultrasensitive, negative feedback control- ling topology with the ultrasensitivity arising from zero-order amino acid kinetics and the negative feedback from ppGpp-controlled ribosome synthesis. In addition, together with the time-scale separation between slow ribosome kinetics and fast turnovers of ppGpp and amino acids, the network topology confers the organism an optimization mechanism which mimics sliding mode control, a nonlinear optimization strategy that is widely used in man-made systems. We further showed that such a controlling mechanism is robust against parameter variations and molecular fluctuations, and is also efficient for biomass production over time. Furthermore, this work elucidates the fundamental controlling mechanism of E. coli proteome allocation, thereby providing insights into quantitative microbial physiology as well as the design of synthetic gene networks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Entropy Engineering and Tunable Magnetic Order in the Spinel High-Entropy Oxide

Spinel oxides are an ideal setting to explore the interplay between configurational entropy, site selectivity, and magnetism in high-entropy oxides (HEOs). In this work, we characterize the magnetic properties of the spinel (Cr, Mn, Fe, Co, Ni) 3 O 4 and study the evolution of its magnetism as a function of nonmagnetic gallium substitution. Across the range of compositions studied here, from 0 to 40% Ga, magnetic susceptibility and powder neutron diffraction measurements show that ferrimagnetic order is robust in the spinel HEO. However, we also find that the ferrimagnetic order is highly tunable, with the ordering temperature, saturated and sublattice moments, and magnetic hardness all varying significantly as a function of Ga concentration. Through X-ray absorption and magnetic circular dichroism, we are able to correlate this magnetic tunability with strong site selectivity between the various cations and the tetrahedral and octahedral sites in the spinel structure. In particular, we find that while Ni and Cr are largely unaffected by the substitution with Ga, the occupancies of Mn, Co, and Fe are each significantly redistributed. Ga substitution also requires an overall reduction in the transition metal valence, and this is entirely accommodated by Mn. Finally, we show that while site selectivity has an overall suppressing effect on the configurational entropy, over a certain range of compositions, Ga substitution yields a striking increase in the configurational entropy and may confer additional stabilization. In conclusion, spinel oxides can be tuned seamlessly from the low-entropy to the high-entropy regime, making this an ideal platform for entropy engineering.

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

Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying

2-Thiouridine (s 2 U) is a nucleobase modification that confers enhanced efficiency and fidelity both on modern tRNA codon translation and on nonenzymatic and ribozyme-catalyzed RNA copying. We have discovered an unusual base pair between two 2-thiouridines that stabilizes an RNA duplex to a degree that is comparable to that of a native A:U base pair. High-resolution crystal structures indicate similar base-pairing geometry and stacking interactions in duplexes containing s 2 U:s 2 U compared to those with U:U pairs. Notably, the C=O···H–N hydrogen bond in the U:U pair is replaced with a C=S···H–N hydrogen bond in the s 2 U:s 2 U base pair. The thermodynamic stability of the s 2 U:s 2 U base pair suggested that this self-pairing might lead to an increased error frequency during nonenzymatic RNA copying. However, competition experiments show that s 2 U:s 2 U base-pairing induces only a low level of misincorporation during nonenzymatic RNA template copying because the correct A:s 2 U base pair outcompetes the slightly weaker s 2 U:s 2 U base pair. In addition, even if an s 2 U is incorrectly incorporated, the addition of the next base is greatly hindered. This strong stalling effect would further increase the effective fidelity of nonenzymatic RNA copying with s 2 U. Our findings suggest that s 2 U may enhance the rate and extent of nonenzymatic copying with only a minimal cost in fidelity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗