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DOE OSTI2025

Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis

A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but trade-offs between accuracy and computational cost have limited their use. We previously developed extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) methods that leverage a negligible compromise in accuracy to substantially decrease the cost of QMD simulations. Here, we develop a reactive QMD approach using the latest XL-BOMD formulation, which enables efficient simulations of highly reactive systems, and use it to investigate mechanisms of intermediate formation in isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenyl isocyanide, forming a thioimidate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation and suggested a possible role of Asp17 as a proton donor in the early phase of ICH catalysis. To test whether the pathway seen using the reactive QMD approach might be relevant to ICH catalysis, we performed X-ray crystallography and pre-steady-state enzyme kinetics studies of wild-type and D17N mutant ICH. Both the structure and kinetics are sensitive to the D17N mutation in a manner that is consistent with the order of the reaction steps seen in the simulations. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate model reactions for the design of experiments that provide information about enzyme mechanisms involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Model-based iterative reconstruction with adaptive regularization for artifact reduction in electron tomography

Obtaining high-quality 3D reconstructions from electron tomography of crystalline particles embedded in lighter support elements is crucial for various material systems such as catalysts for fuel cell applications. However, significant challenges arise due to the limited tilt range, sparse and low signal-to-noise ratio of the measurements. In addition, small metal particles can cause strong streaking and shading artifacts in the 3D reconstructions when using conventional reconstruction algorithms due to the presence of Bragg diffraction and the large scattering cross-section difference between the materials of the particles and the background support regions. These artifacts lead to errors in the downstream characterization affecting extraction of critical features such as the size of the metal particles, their distribution and the volume of the lighter support regions. In this paper, we present a two-stage algorithm based on metal artifact reduction, utilizing model-based iterative reconstruction methods with adaptive adjustment of regularization parameters. Our approach yields high-quality 3D reconstructions compared to traditional algorithms, accurately capturing both the metal particles as well as the background support. We demonstrate the effectiveness of our algorithm through simulated and experimental bright-field electron tomography data, showing significant improvements in reconstruction quality compared to traditional methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Catalytic enhancement in the performance of the microscopic two-stroke heat engine

Here we consider a model of heat engine operating in the microscopic regime: the two-stroke engine. It produces work and exchanges heat in two discrete strokes that are separated in time. The working body of the engine consists of two d-level systems initialized in thermal states at two distinct temperatures. Additionally, an auxiliary nonequilibrium system called catalyst may be incorporated with the working body of the engine, provided the state of the catalyst remains unchanged after the completion of a thermodynamic cycle. This ensures that the work produced by the engine arises solely from the temperature difference. Upon establishing the rigorous thermodynamic framework, we characterize twofold improvement stemming from the inclusion of a catalyst. Firstly, we prove that in the noncatalytic scenario, the optimal efficiency of the two-stroke heat engine with a working body composed of two-level systems is given by the Otto efficiency, which can be surpassed by incorporating a catalyst with the working body. Secondly, we show that incorporating a catalyst allows the engine to operate in frequency and temperature regimes that are not accessible for noncatalytic two-stroke engines. We conclude with a general conjecture about the advantage brought by a catalyst: including the catalyst with the working body always allows to improve efficiency over the noncatalytic scenario for any microscopic two-stroke heat engines. We prove this conjecture for two-stroke engines where the working body is composed of two d-level systems initialized in thermal states at two distinct temperatures, as long as the final joint state leading to optimal efficiency in the noncatalytic scenario is not a product state, or at least one of the d-level system is not thermal.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS2000

Applications of Low Density Flow Techniques and Catalytic Recombination at the Johnson Space Center

The talk presents a brief background on defInitions of catalysis and effects associated with chemically nonequilibrium and low-density flows of aerospace interest. Applications of catalytic recombination on surfaces in dissociated flow are given, including aero heating on reentry spacecraft thermal protection surfaces and reflection of plume flow on pressure distributions associated with the space station. Examples include aero heating predictions for the X-38 test vehicle, the inlet of a proposed gas-sampling probe used in high enthalpy test facilities, and a parabolic body at angle of attack. The effect of accommodation coefficients on thruster induced pressure distributions is also included. Examples of tools used include simple aero heating formulas based on boundary layer solutions, an engineering approximation that uses axisymmetric viscous shock layer flow to simulate full three dimensional flow, full computational fluid dynamics, and direct simulation Monte-Carlo calculations. Methods of determining catalytic recombination rates in arc jet flow are discus ed. An area of catalysis not fully understood is the formation of single-wall carbon nanotubes (SWNT) with gas phase or nano-size metal particles. The Johnson Space Center is making SWNTs using both a laser ablation technique and an electric arc vaporization technique.

Scott, Carl D.↗

NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and tRNA(Gln): ATP:glnRS complexes. The trinucleotide CCA of the 3'-end tRNA is placed into the active site pocket of tyrRS, based on the scheme of interaction between tRNA(Gln) and glnRS, and upon the stereochemistry of the tyrRS:tRNA:Tyr-AMP transition state. This provides a model of the non-specific recognition of a tRNA's 3'-end by an aRS, which might be similar to that of the ancestral aRS's. In the next step, modeling of the rest of the acceptor stem of tRNA (Tyr) with tyrRS is carried out.

Rein, Robert↗

NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗

DOE OSTI2025

Spectroscopic and Computational Studies of Spin-Orbit Coupling of Lanthanide Oxides

Spin-orbit (SO) coupling makes it possible for spin forbidden transitions or reactions within non-relativistic quantum theory feasible. Thus, quantification of such interactions has important implications in photophysics and chemical catalysis. This work aims to quantify SO interactions using lanthanide (Ln) oxides as target molecular systems. Through these systems, we examine the impact on the SO coupling by electron configurations and 4f orbital occupancies of Ln elements and sizes of the metal oxides. By examining these factors, we explore how SO coupling is affected by the number of Ln 4f electrons for a given size of molecules and if the Ln 4f orbitals remain atomic in nature in these small clusters. Ln oxides are produced in laser ablation molecular beams, identified with time-of-fight mass spectrometry, and characterized with laser spectroscopy and relativistic quantum chemical computations. Spectroscopic measurements include mass-analyzed threshold ionization (MATI), zero electron kinetic energy, and slow electron velocity-map imaging spectroscopies. Relativistic computations treat scalar relativistic corrections, electron correlations, and SO interactions. The main results are SO terms and energies of the neutral molecules and singly charged cations, ionization energies of the neutral species, metal-metal and metal-oxygen vibrational frequencies of the ions and, in some cases, neutrals as well, and charge effects on the bonding and structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

ReactionMechanismSimulator.jl: A modern approach to chemical kinetic mechanism simulation and analysis

Abstract We present ReactionMechanismSimulator.jl (RMS), a modern differentiable software for the simulation and analysis of chemical kinetic mechanisms, including multiphase systems. RMS has already been applied to problems in combustion, pyrolysis, polymers, pharmaceuticals, catalysis, and electrocatalysis. RMS is written in Julia, making it easy to develop and allowing it to take advantage of Julia's extensive numerical computing ecosystem. In addition to its extensive library of optimized analytic Jacobians, RMS can generate and use Jacobians computed using automatic differentiation and symbolically generated analytic Jacobians. RMS is demonstrated to be faster than Cantera and Chemkin in several benchmarks. RMS also implements an extensive set of features for analyzing chemical mechanisms, including a library of easy‐to‐call plotting functions, molecular structure resolved flux diagram generation, crash analysis, traditional sensitivity analysis, transitory sensitivity analysis, and an automatic mechanism analysis toolkit. RMS implements efficient adjoint and parallel forward sensitivity analyses. We also demonstrate the ease of adding new features to RMS.

Johnson, Matthew S.↗

NASA NTRS1997

Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.

NASA Discipline Exobiology↗

DOE OSTI2025

A Perspective on Multiscale Modeling of Explicit Solvation-Enabled Simulations of Catalysis at Liquid–Solid Interfaces

Catalysis at liquid-solid interfaces is profoundly influenced by the interfacial solvent structure, which affects catalytic activity, selectivity, and reaction pathways. This perspective discusses state-of-the-art multiscale modeling methods that integrate quantum mechanics and molecular mechanics approaches to apply explicit solvent molecules to capture these interfacial phenomena. Specifically, the construction of multiscale models, the importance of capturing the interfacial solvent structure, and the computational strategies used to achieve this are explored, and the challenges in balancing chemical accuracy with computational expense are highlighted. Additionally, this perspective addresses the limitations of current methods. Opportunities for integrating machine learning are proposed. Here, by advancing the efficiency and user friendliness of multiscale modeling, it is argued that deeper insights into heterogeneous catalysis in liquid phases can be provided, which will ultimately contribute to the development of more efficient catalytic processes.

Ab initio molecular dynamics↗

NASA NTRS1978

A numerical solution of the Navier-Stokes equations for chemically nonequilibrium, merged stagnation shock layers on spheres and two-dimensional cylinders in air

Results of solving the Navier-Stokes equations for chemically nonequilibrium, merged stagnation shock layers on spheres and two-dimensional cylinders are presented. The effects of wall catalysis and slip are also examined. The thin shock layer assumption is not made, and the thick viscous shock is allowed to develop within the computational domain. The results show good comparison with existing data. Due to the more pronounced merging of shock layer and boundary layer for the sphere, the heating rates for spheres become higher than those for cylinders as the altitude is increased.

Johnston, K. D.↗

NASA NTRS1995

Analytical studies of hypersonic viscous dissociated flows

This project primarily dealt with integral boundary-layer solution techniques that are directly applicable to the problem of determining aerodynamic heating rates of hypersonic vehicles like X-33 in the vicinity of stagnation points, windward centerlines, and swept-wing leading edges. The analyses include effects of finite-rate gas chemistry across the boundary layer and finite-rate catalysis of atom recombination at the surface. A new approach for combining the insight afforded by integral boundary-layer analysis with comprehensive (and expensive) computational fluid dynamic (CFD) flowfield solutions of the thin-layer Navier-Stokes equations was developed. The approach extracts CFD derived quantities at the wall and at the boundary layer edge for inclusion in a post-processing boundary-layer analysis. The post-processed data base allows a designer at a workstation to ask and answer the following questions: (1) How much does the heating change if one uses a thermal protection system (TPS) with different catalytic properties than was used in the original CFD solution? (2) How does the heating change when one moves the interface of two different TPS materials with different catalytic efficiencies for the purpose of reducing vehicle weight and expense? The answer to the second question is particularly critical, because abrupt changes from low catalytic efficiency to high catalytic efficiency can lead to localized increase in heating which exceeds the usually conservative estimate provided by a fully catalytic wall assumption. A secondary issue that was addressed involves the prediction of heating levels in the vicinity of sharp corners that are transverse to or aligned with the flow. An example of the first case is heating at the edge of the COMET reentry module. An example of the second case is heating along the side edge of a deflected body flap on an SSV. The difficulty of putting grids in the vicinity of such corners with continuously varying metric coefficients causes problems in CFD predictions. A preliminary theory for prediction that says the heating at the corner is X percent of the heating N boundary-layer thicknesses inboard was developed. This will prove useful to analytically evaluate the possible benefits of rounding the edges of these configurations and defining how much rounding is sufficient.

Inger, George R.↗

NASA NTRS1993

Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

Manchester, John I.↗

NASA NTRS2002

Heats of Segregation and Segregation Profiles of BCC Metals

The composition of metal alloy surfaces is often different from that of the bulk. Some alloys exhibit surface segregation, where one or more species reside preferentially at or near the surface. A detailed understanding of this behavior is necessary to correctly model such phenomena as adhesion or catalysis. Several phenomenological approaches to the problem have been put forward, falling into two broad categories: Thermodynamic approaches, where the equilibrium distribution of chemical species is computed. Atomistic approaches, where the tendency of a species to segregate is determined by computation of the energies of single atoms of that species in bulk and surface environments.

Good, Brian S.↗

NASA NTRS1991

Effect of non-equilibrium flow chemistry and surface catalysis on surface heating to AFE

The effect of nonequilibrium flow chemistry on the surface temperature distribution over the forebody heat shield on the Aeroassisted Flight Experiment (AFE) vehicle was investigated using a reacting boundary-layer code. Computations were performed by using boundary-layer-edge properties determined from global iterations between the boundary-layer code and flow field solutions from a viscous shock layer (VSL) and a full Navier-Stokes solution. Surface temperature distribution over the AFE heat shield was calculated for two flight conditions during a nominal AFE trajectory. This study indicates that the surface temperature distribution is sensitive to the nonequilibrium chemistry in the shock layer. Heating distributions over the AFE forebody calculated using nonequilibrium edge properties were similar to values calculated using the VSL program.

Stewart, David A.↗

NASA NTRS2012

Influence of Catalysis and Oxidation on Slug Calorimeter Measurements in Arc Jets

Arc jet tests play a critical role in the characterization and certification of thermal protection materials and systems (TPS). The results from these arc jet tests feed directly into computational models of material response and aerothermodynamics to predict the performance of the TPS in flight. Thus the precise knowledge of the plasma environment to which the test material is subjected, is invaluable. As one of the environmental parameters, the heat flux is commonly measured. The measured heat flux is used to determine the plasma enthalpy through analytical or computational models. At NASA Ames Research Center (ARC), slug calorimeters of a geometrically similar body to the test article are routinely used to determine the heat flux. A slug calorimeter is a thermal capacitance-type calorimeter that uses the temperature rise in a thermally insulated slug to determine the heat transfer rate, see Figure 1(left). Current best practices for measuring the heat flux with a slug calorimeter are described in ASTM E457 - 96. Both the calorimeter body and slug are made of Oxygen Free High Conductivity Copper, and are cleaned before each run.

Nawaz, Anuscheh↗

NASA NTRS2024

Two mechanisms for the spontaneous emergence, execution, and reprogramming of chemical logic circuits

A key question in origin-of-life research is how primitive life or life-like systems obtained reusable and reprogrammable machinery of processing information to respond to various environmental and internal stimuli. One strategy to approach this question is to view living systems as universal chemical computers. This approach focuses upon uncovering how reusable and reprogrammable chemical NOT, AND, and OR logic gates could appear under prebiotically possible scenarios where simple chemicals and second- or lower-order reactions are more frequent than macromolecules and higher-order reactions. In this article, we theoretically model two generic mechanisms of forming Boolean gates based on geochemically plausible reaction systems that could have preceded complex biopolymers. The mechanisms exploit simple bistable autocatalytic systems to encode binary variables and use heterogeneous dilution rates to differentially activate or deactivate autocatalysis in different reactors. We found that NOT, AND, and OR gates, as well as more complex logic circuits, can spontaneously arise from connected, well-mixed flow reactors based on (i) catalysis by a heterodimer between mutually inhibitory autocatalysts or (ii) selectively permeable tunnels connecting reactors. Our results suggest that simple machinery can support the prebiotic emergence of complex chemical logic circuits and provide new guides for experimentally actualizing chemical computation.

Zhen Peng↗

DOE OSTI2026

Continuity of reaction kinetics across the pressure and materials gaps in CO oxidation on FeO–Pt interfaces

Translating atomic-scale insights from surface science studies of model catalysts to practical powder catalysts remains a persistent challenge in heterogeneous catalysis. Here, in this study, we demonstrate mechanistic continuity across the pressure and materials gaps during CO oxidation at the FeO-Pt interface using in situ microscopy, spectroscopy and computational modelling. Under reaction conditions, coordinatively unsaturated Fe (Fe cus ) sites at the interface enable selective O 2 activation on CO-saturated surfaces, circumventing the CO-poisoning limitation of platinum-group metals. We identify parallel reaction pathways involving the *O 2 -*CO intermediate. Remarkably, activation energies remain consistent at 12-15 kJ mol −1 (0.12-0.16 eV) from ultrahigh vacuum to atmospheric pressures and from FeO/Pt(111) model catalysts to FeO/Pt powder catalysts, validating mechanistic insights derived from surface science studies. Our findings show an example of bridging the long-standing divide between model and practical catalyst systems, establishing an effective approach to capture catalytic behaviours under operational conditions and advancing mechanism-driven catalyst design.

03 NATURAL GAS↗