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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids

Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics. Extension of this force field to new peptoid side chains has historically required reparameterization of side chain bonded interactions against ab initio data. This fitting protocol improves the accuracy of the force field but is also burdensome and precludes modular extensibility of the model to arbitrary peptoid sequences. In this work, we develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID) as an extension of CGenFF-NTOID employing a modular decomposition of the peptoid backbone and side chain parameterizations, wherein arbitrary side chains within the large family of substituted methyl groups (i.e., –CH 3 , –CH 2 R, –CHRR', and –CRR'R") are directly ported from CGenFF. We validate this approach against ab initio calculations and experimental data to develop a MoSiC-CGenFF-NTOID model for all 20 natural amino acid side chains along with 13 commonly used synthetic side chains and present an extensible paradigm to efficiently determine whether a novel side chain can be directly incorporated into the model or whether refitting of the CGenFF parameters is warranted. We make the model freely available to the community along with a tool to perform automated initial structure generation.

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

Probing the influence of ion-pairing on ligand-field excited-state dynamics

Exploration of the photophysical and photochemical properties of transition metal complexes has driven ground-breaking advancements in solar energy conversion technologies, including photoredox catalysis. While significant research has been devoted to understanding excited state properties of second- and third-row transition metal complexes, earth-abundant first-row metal complexes have received comparatively little attention in this context until very recently. In particular, the role of ion-pairing – which has been identified as a potentially significant factor for Ir(III)-based photosensitizers – has not been examined with regard to its influence on the ligand-field excited states that dominate much of first-row photophysics. A key challenge in studying ion-pair interactions lies in quantifying the extent and nature of ion-pairing, particularly in non-aqueous media where the vast majority of photophysical studies are performed. Cobalt(III) polypyridyl complexes provide an attractive platform to address such questions due to their demonstrated potential for applications in photoredox catalysis involving ligand-field excited states. In the present study, we prepared a cobalt(III) polypyridyl complex, [Co(4,4′-OMebpy) 3 ](BAr F 4 ) 3 (where 4,4′-OMebpy is 4,4′-dimethoxy-2,2′-bipyridine and BAr F 4 is tetrakis(3,5-bis(trifluoromethyl)-phenyl)borate) to probe ion-pairing in non-aqueous solutions. Specifically, analysis of data acquired from both variable-temperature diffusion ordered spectroscopy (DOSY) NMR and 1-D rotating-frame nuclear Overhauser effect (ROE) experiments allowed us to identify and differentiate between solvent-separated ion pairs in high-dielectric media and contact ion pairs in a low-dielectric solvent. Time-resolved absorption spectroscopy was then used to measure ground-state recovery dynamics under these varying conditions of ion-pairing, the results of which revealed an increase in excited-state lifetime for contact ion-pairs that we suggest arises from a reduction in outer-sphere reorganization energy relative to conditions which favored solvent-separated ion pairs. We believe this study demonstrates that one can leverage broadly available NMR-based methods to understand ion-pairing in non-aqueous solutions, which in turn can provide a microscopic picture of intermolecular interactions that can impact the photophysical properties of transition metal-based chromophores.

Ghosh, Atanu [Michigan State University, East Lans↗
DOE OSTI2020

The energetics and dynamics of confinement in flexible frameworks and molecular confinement

This project is part of an ongoing and long-term collaboration among Alexandra Navrotsky (who moved recently from UC Davis to Arizona State University), Nancy Ross at Virginia Tech, and Brian Woodfield at Brigham Young University (BYU) on the thermodynamics and lattice dynamics of nanophase and porous materials. Navrotsky emphasizes energetics of formation and guest molecule sorption by ambient and high temperature calorimetry, Woodfield contributes cryogenic heat capacity measurements, and Ross uses inelastic neutron scattering, X-ray and neutron diffraction, and high pressure studies to probe lattice dynamics and phase transitions. Porous frameworks form the chemical and structural basis for critical technologies in separations, catalysis, nuclear waste containment and biomedical applications. Hundreds of zeolites and metal organic frameworks (MOFs) have been synthesized, and their ability to separate and store hydrogen, methane and carbon dioxide has been investigated both experimentally and theoretically. Nevertheless, a fundamental and systematic molecular-level understanding of the thermodynamic and structural factors governing the stability and guest-host interactions in these materials lags behind focused studies of specific systems. Because the guest molecules interact with each other and with the host framework, molecular confinement is a finely balanced and complex phenomenon. The ability of the guest molecules to bind and diffuse through the pores is determined by the nature of the host framework which, in turn, responds to the nature and concentration of guest molecules and to pressure and temperature. The work explores how framework flexibility, tailored by structure, composition, temperature and pressure, is a general phenomenon, similar in nature but variable in extent, in both zeolites and MOFs and is part of a free energy landscape in which framework-guest interactions, pressure, and temperature result in changes in framework geometry and, in some cases, phase transitions. These subtle and/or pronounced changes in lattice geometry, energetics, and dynamics can play a decisive role in confinement and in differentiating the binding of molecules of similar size.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Machine-Learned Force Field for Molecular Dynamics Simulations of Nonequilibrium Ammonia Synthesis on Iron Catalysts

Ammonia (NH 3 ) is one of the most important industrial chemicals. The conventional NH 3 synthesis method-the Haber–Bosch process-converts atmospheric nitrogen (N 2 ) into NH 3 using H 2 with an iron (Fe) catalyst. However, this process requires high pressures (100–200 atm) and temperatures (700–800 K) near thermal equilibrium. Recently, Fe-based nanocatalysts have been reported to produce promising NH 3 yields under atmospheric pressures and temperature-modulated nonequilibrium conditions. Understanding the mechanism of nonequilibrium catalysis with programmed temperature variation could help to optimize this fully electrified and less energy-intensive process. Although reactive molecular dynamics (RMD) simulations can be a useful tool to model nonequilibrium catalytic processes, they require the development of accurate force fields (i.e., interatomic potentials). Here, we present a machine-learned (ML) force field within the Deep Potential MD (DPMD) framework, trained using periodic density functional theory (DFT) calculations, to model NH 3 synthesis on Fe catalysts with various surface adsorbates such as *N, *H, *N 2 , *H 2 , *NH, *NH 2 , and *NH 3 . Here, we generated the DFT data from static models of elementary reactions on the most stable (110) surface of body-centered cubic Fe, which then were augmented by data from constant number of particles–volume–temperature (NVT) DFT-MD trajectories at various temperatures. Finally, we utilized the fully optimized ML force field to investigate reaction dynamics at an Fe(110) surface at linearly increasing temperatures using NVT-DPMD simulations. Our simulations indicate that pulsed temperature ramping could prove favorable for NH3 synthesis. For example, we conducted ramping under multiple sets of conditions: (i) from 900 to 1200 K over periods of 0.1–0.3 ns for Fe surfaces precovered with N or NH along with H; and (ii) from 300 to 600 K over 0.1–0.3 ns for Fe surfaces precovered with NH 3 . While our simulations so far are limited to short time scales (very rapid heating), these observations shed light on the mechanism of the high NH 3 synthesis rate achieved in a novel temperature-modulated nonequilibrium catalytic reactor using pulsed heating and cooling.

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

Dynamic Evolution of Palladium Single Atoms on Anatase Titania Support Determines the Reverse Water–Gas Shift Activity

Research interest in single-atom catalysts (SACs) has been continuously rising. However, the lack of understanding of the dynamic behaviors of SACs during applications hinder catalyst development and mechanistic understanding. Herein, we report on the evolution of active sites over Pd/TiO 2 -anatase SAC (Pd 1 /TiO 2 ) in the reverse water-gas shift (rWGS) reaction. Combining kinetics, in-situ characterization, and theory, we show that at T ≥ 350 °C, the reduction of TiO 2 by H 2 alters the coordination environment of Pd, creating Pd sites with partially cleaved Pd-O interfacial bonds and a unique electronic structure that exhibit high intrinsic rWGS activity through the carboxyl pathway. The activation by H 2 is accompanied by the partial sintering of single Pd atoms (Pd 1 ) into disordered, flat, ~1 nm diameter clusters (Pd n ). The highly active Pd sites in the new coordination environment under H 2 are eliminated by oxidation, which, when performed at high temperature, also re-disperses Pd n and facilitates the reduction of TiO 2 . In contrast, Pd 1 sinters into crystalline, ~5 nm particles (Pd NP ) during CO treatment, deactivating Pd 1 /TiO 2 . During the rWGS reaction, the two Pd evolution pathways co-exist. The activation by H 2 dominates, leading to the increasing rate with time-on-stream, and steady-state Pd active sites similar with the ones formed under H 2 . Finally, this work demonstrates how the coordination environment and nuclearity of metal sites on a SAC evolve during catalysis and pre-treatments, and how their activity is modulated by these behaviors. These insights on SAC dynamics and structure-function relationship are valuable to mechanistic understanding and catalyst design.

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

Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds

Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization has been proposed to play a role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of proton mobility in H-bonds. We used neutron crystallography, atomic resolution X-ray bond length analysis, and large quantum mechanics/molecular mechanics-Born–Oppenheimer molecular dynamics (QM/MM-BOMD) simulations to comprehensively characterize the shared proton/deuteron in a Glu–Asp low-barrier hydrogen bond (LBHB) in the bacterial protein YajL that is a conventional H-bond in the homologous disease-associated human protein DJ-1. X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid near a cysteine thiolate. Residues in an H-bonded network that might favor LBHB formation in YajL were interrogated by the mutation of homologous residues in DJ-1. A distal DJ-1 substitution increases proton delocalization in the Glu–Asp H-bond, demonstrating that mutations within extended H-bond networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds. In addition, proton mobility in the H-bond is correlated with dimer-spanning motions in the QM/MM-BOMD simulations of YajL and DJ-1. Our results show that proton delocalization can be tuned using combined bioinformatic, structural, and computational information, opening the possibility of using engineered proton delocalization as a probe of H-bonding environments and as a tool to test hypotheses about LBHB function.

Lin, Jiusheng [University of Nebraska, Lincoln, NE↗
DOE OSTI2021

Hydration structure of flat and stepped MgO surfaces

We investigate the solvation structure of flat and stepped MgO(001) in neutral liquid water using ab initio molecular dynamics based on a hybrid density functional with dispersion corrections. Our simulations show that the MgO surface is covered by a densely packed layer of mixed intact and dissociated adsorbed water molecules in a planar arrangement with strong intermolecular H-bonds. The water dissociation fractions in this layer are >20% and >30% on the flat and stepped surfaces, respectively. Slightly above the first water layer, we observe metastable OH groups perpendicular to the interface, similar to those reported in low temperature studies of water monolayers on MgO. Here, these species receive hydrogen bonds from four nearby water molecules in the first layer and have their hydrophobic H end directed toward bulk water, while their associated protons are bound to surface oxygens. The formation of these OH species is attributed to the strong basicity of the MgO surface and can be relevant for understanding various phenomena from morphology evolution and growth of (nano)crystalline MgO particles to heterogeneous catalysis.

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

Probing Pore Size and Connectivity in Porous Silicas Using 13C MAS NMR Spectroscopy of Supercritical Methane

Measuring the pore size and pore-size distributions and exploring the fluid-exchange dynamics between different types of pores in porous materials remains a significant experimental challenge but is critical to understanding catalysis, chromatography, nutrient cycling, and a whole range of geochemical phenomena, including shale gas and tight gas extraction. Here, we present the results of 1D 13 C NMR and 2D exchange spectroscopy (EXSY) NMR investigations of a porous silica using supercritical methane (scCH 4 ) as a direct probe of pore size and fluid exchange between pore types. The results show that the 13 C chemical shift of scCH 4 adsorbed in nanometer-scale silica pores becomes more negative with increasing pore diameter, in agreement with trends reported for gas hydrates, zeolites, MOFs, and clays and other microporous (<10 nm pores) geochemical materials. These 13 C chemical shifts follow a natural log–linear trend with pore size in the vacuum-dried porous silicas studied here, allowing one to predict pore size based on the 13 C chemical shift in dry silica nanopores. The EXSY and 1D 13 C NMR results both show that CH 4 exchanges between pore and bulk fluid environments over rate scales from 0.01 to 1 kHz in vacuum-dried samples and that exchange dynamics must be considered when interpreting 13 C NMR of pore-adsorbed CH 4 . Introducing H 2 O to the system causes the 13 C chemical shift to become more negative with increasing H 2 O content as a result of H 2 O preferentially filling small pores, forcing CH 4 to occupy larger pores that are better connected to the bulk environment. Likewise, the 1D 13 C data show a decreased distribution of exchange rates between pore-adsorbed and bulk CH 4 in the presence of H 2 O.

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

Applying deep learning methods to develop new models of molecular charge transfer, nonadiabatic dynamics, and nonlinear spectroscopy in the condensed phase

Photon- and field-induced charge transfer has central importance in the generation and storage of electricity, the novel properties of materials, photo-induced catalysis, and electro-optic activity (e.g., photovoltaic cells, fuel cells, and organic chromophores for use in optical fibers and light-emission diodes). These non-equilibrium electronic and chemical transformations are probed by ultrafast, nonlinear spectroscopies. Accurate simulations play a crucial role in our ability to understand, optimize, and control these transformations. This project applies modern deep learning and machine learning (ML) methods to dramatically improve models of electronic dynamics, electronic-nuclear dynamics, and spectroscopic measurements for improved simulations of chemistry in complex environments, far from equilibrium phenomena, and processes in extreme environments, such as materials exposed to strong or resonant fields. This project develops accurate neural net models that go beyond predictive capability to also provide new insight into the fundamental physics underlying electron and nuclear dynamics. To achieve its objectives, this project explores and develops customized versions of high-capacity deep learning algorithms/models. These techniques are developed with an emphasis on fundamental chemical insight, not just predictive accuracy, to assist the development of the next generation of quantum simulation methods.

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

Dynamic Behavior of Platinum Atoms and Clusters in the Native Oxide Layer of Aluminum Nanocrystals

Strong metal–support interactions (SMSIs) are well-known in the field of heterogeneous catalysis to induce the encapsulation of platinum (Pt) group metals by oxide supports through high temperature H 2 reduction. However, demonstrations of SMSI overlayers have largely been limited to reducible oxides, such as TiO 2 and Nb 2 O 5 . In this report we show that the amorphous native surface oxide of plasmonic aluminum nanocrystals (AlNCs) exhibits SMSI-induced encapsulation of Pt following reduction in H 2 in a Pt structure dependent manner. Reductive treatment in H 2 at 300 °C induces the formation of an AlO x SMSI overlayer on Pt clusters, leaving Pt single-atom sites (Ptiso) exposed available for catalysis. The remaining exposed Pt iso species possess a more uniform local coordination environment than has been observed on other forms of Al 2 O 3 , suggesting that the AlO x native oxide of AlNCs presents well-defined anchoring sites for individual Pt atoms. This observation extends our understanding of SMSIs by providing evidence that H 2 -induced encapsulation can occur for a wider variety of materials and should stimulate expanded studies of this effect to include nonreducible oxides with oxygen defects and the presence of disorder. It also suggests that the single-atom sites created in this manner, when combined with the plasmonic properties of the Al nanocrystal core, may allow for site-specific single-atom plasmonic photocatalysis, providing dynamic control over the light-driven reactivity in these systems.

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

Capturing Surface Coverage Effects in Heterogeneous Catalysis

Adsorbate–adsorbate lateral interactions at relevant surface coverages have a significant effect on chemical kinetics, thereby influencing the activity of a heterogeneous catalyst. Coverage-dependent kinetic and thermodynamic parameters therefore must be included in studies of such complex systems to properly predict the turnover frequencies and kinetic trends. Thus, it becomes extremely important to accurately capture the strength of lateral interactions between neighboring species under realistic reaction conditions. In this Perspective, we discuss the various existing computational and experimental methods for determining adspecies coverage and configurational effects. The choice of the tools and methods employed in such studies depends on factors such as time, length scales, computational cost, the presence of solvents, and reaction conditions. The applications of each method and the respective challenges are also discussed here. As a result, we discuss the recent developments and future of the state-of-the-art for inclusion of surface coverage and configuration into a holistic picture for accurate predictions of catalytic behavior.

09 BIOMASS FUELS↗
DOE OSTI2024

Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms

Abstract Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant unusually preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employ static and dynamic structural methods and observe that, compared to R132H, the R132Q active site adopts a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling reveals a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Coherent charge hopping suppresses photoexcited small polarons in ErFeO 3 by antiadiabatic formation mechanism

Polarons are prevalent in condensed matter systems with strong electron-phonon coupling. The adiabaticity of the polaron relates to its transport properties and spatial extent. To date, only adiabatic small polaron formation has been measured following photoexcitation. The lattice reorganization energy is large enough that the first electron–optical phonon scattering event creates a small polaron without requiring substantial carrier thermalization. We measure that frustrating the iron-centered octahedra in the rare-earth orthoferrite ErFeO 3 leads to antiadiabatic polaron formation. Coherent charge hopping between neighboring Fe 3+ –Fe 2+ sites is measured with transient extreme ultraviolet spectroscopy and lasts several picoseconds before the polaron forms. The resulting small polaron formation time is an order of magnitude longer than previous measurements and indicates a shallow potential well, even in the excited state. The results emphasize the importance of considering dynamic electron-electron correlations, not just electron-phonon–induced lattice changes, for small polarons for transport, catalysis, and photoexcited applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Transient Catalytic Reaction Analysis Through Signal Defragmentation

The Temporal Analysis of Products (TAP) pulse response technique provides valuable insights into catalytic function and reaction kinetics. However, complex fragmentation patterns in the TAP mass spectrometry signals can complicate precise quantification, particularly when analyzing transient gas flux data typical of TAP experiments. This work demonstrates a standard defragmentation method that deconvolves transient TAP signals while maintaining the temporal resolution of the experiment. First, the integrals of calibration gas fluxes are used to determine the fingerprint fragmentation pattern and construct a fragmentation matrix. This matrix is then used to defragment experimental flux data at each recorded time point via a non-negative least squares regression. The effectiveness of this method is demonstrated using virtual data and control experiments with a TAP reactor system. The defragmentation is then applied to the more complex propane dehydrogenation reaction on a chromia/alumina catalyst, which can contain up to ten significant gas species in the reactor outlet. Initial propane pulsing reveals an induction period during which propane is fully oxidized to CO2, followed by partial reduction to CO. Afterwards, there is a transition in chemistries towards coking and propylene production. Our example illustrates a practical method for the accurate determination of the time-dependent reactant/product concentrations and rates for a thorough analysis of the propane dehydrogenation kinetics. This approach can be broadly applied to any transient mass spectrometry experiment for a better understanding of catalyst-reaction dynamics.

36 - MATERIALS SCIENCE↗
DOE OSTI2022

Quantifying transport and electrocatalytic reaction processes in a gastight rotating cylinder electrode reactor via integration of Computational Fluid Dynamics modeling and experiments

Understanding the complexity of the multiple processes of mass, momentum, charge, and heat transport, and how these affect reaction kinetics at the electrode/electrolyte interface is one of the major challenges in the field of energy and catalysis. The rapid and rational scale-up of electrocatalytic systems to industrial scales require a detailed understanding of nonlinear transport-reaction processes, accessible only through the building of multi-physics models that capture with high fidelity the complexity of real-world devices. The gastight rotating cylinder electrode (RCE) reactor is a promising lab-scale tool that can decouple transport from intrinsic kinetics to generate data for first-principle models useful in the design of industrial, electrochemical reactors. Computational Fluid Dynamics (CFD) studies have previously been used to investigate the bulk flow in RCE reactors for simple corrosion and electroplating processes. However, the quantification of changes in local concentration within the viscous layer where catalysis takes place requires capturing the correct flow conditions inside the hydrodynamic boundary layer near the surface of the electrode. Further, this requires simulations with spatial resolution in the nm and μm scale and temporal resolutions between ms and s scales that are similar to the timescales for reactions on the electrode surface. In this study, experimental electrocatalysis is combined with CFD modeling to elucidate and parameterize the hydrodynamics in a gastight RCE reactor. CFD simulations of the electrochemical ferricyanide reduction reaction under mass transport limited conditions are used to evaluate the validity of the CFD model parameters by comparing calculated dimensionless mass transport descriptors to dimensionless correlations obtained experimentally. Justifications for assumptions and details of the simulation methods used in this study are presented to provide a detailed understanding of the effect that each model parameter has on the ability to accurately simulate electrocatalysis in RCE systems. The simulation methodology reported here is a first step towards the development of multi-scale models for the study of transport dependent electrocatalytic processes, such as the electrochemical transformation of CO 2 to fuels and chemicals.

42 ENGINEERING↗
DOE OSTI2023

Nonorthogonal Cascade Catalysis in Multicompartment Micelles

Multicompartment micelles (MCMs) containing acid and base sites in discrete domains are prepared from poly(norbornene)-based amphiphilic bottlebrush copolymers in aqueous media. Here, the acid and base sites are localized in different compartments of the micelle, enabling the nonorthogonal reaction sequence: deacetalization – Knoevenagel condensation – Michael addition of acetals to 2-amino chromene derivatives. Computational simulations using dissipative particle dynamics (DPD) elucidated the bottlebrush composition required to effectively site-isolate the nonorthogonal catalysts. This contribution presents MCMs as a new class of nanostructures for one-pot multistep nonorthogonal cascade catalysis, laying the groundwork for the isolation of three or more incompatible catalysts to synthesize value-added compounds in a single reaction vessel, in water.

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

Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase

Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid–base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP’s high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.

archaea↗
DOE OSTI2024

Actuating Liquid Crystals Rapidly and Reversibly by Using Chemical Catalysis

Abstract Microtubules and catalytic motor proteins underlie the microscale actuation of living materials, and they have been used in reconstituted systems to harness chemical energy to drive new states of organization of soft matter (e.g., liquid crystals (LCs)). Such materials, however, are fragile and challenging to translate to technological contexts. Rapid (sub‐second) and reversible changes in the orientations of LCs at room temperature using reactions between gaseous hydrogen and oxygen that are catalyzed by Pd/Au surfaces are reported. Surface chemical analysis and computational chemistry studies confirm that dissociative adsorption of H 2 on the Pd/Au films reduces preadsorbed O and generates 1 ML of adsorbed H, driving nitrile‐containing LCs from a perpendicular to a planar orientation. Subsequent exposure to O 2 leads to oxidation of the adsorbed H, reformation of adsorbed O on the Pd/Au surface, and a return of the LC to its initial orientation. The roles of surface composition and reaction kinetics in determining the LC dynamics are described along with a proof‐of‐concept demonstration of microactuation of beads. These results provide fresh ideas for utilizing chemical energy and catalysis to reversibly actuate functional LCs on the microscale.

Chemistry↗