Search NASA⌕ Search

SEARCH · Search NASA

Results for “computational catalysis”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12

Introducing the embedded random phase approximation: H 2 dissociative adsorption on Cu(111) as an exemplar

The random phase approximation (RPA) as a means of treating electron correlation recently has been shown to outperform standard density functional theory (DFT) approximations in a variety of cases. However, the computational cost of the RPA is substantially more than DFT, especially when aiming to study extended surfaces. Properly accounting for sufficient surface ensemble size, Brillouin zone sampling, and vacuum separation of periodic images in standard periodic-planewave-based DFT code raises the cost to achieve converged results. Here, we show that sub-system embedding schemes enable use of the RPA for modeling heterogeneous reactions at reduced computational cost. Further, we explore two different embedded RPA (emb-RPA) approaches, periodic emb-RPA and cluster emb-RPA. We use the (experimentally and theoretically) well-studied H 2 dissociative adsorption on Cu(111) as our exemplar, and first perform full periodic RPA calculations as a benchmark. The full RPA results match well the semi-empirical barrier fit to experimental observables and others derived from high-level computations, e.g., from recent embedded n-electron valence second order perturbation theory [Zhao et al., J. Chem. Theory Comput. 16(11), 7078–7088 (2020)] and quantum Monte Carlo [Doblhoff-Dier et al., J. Chem. Theory Comput. 13(7), 3208–3219 (2017)] simulations. Among the two emb-RPA approaches tested, the cluster emb-RPA accurately reproduces the energy profile (maximum error of 50 meV along the reaction pathway) while reducing the computational cost by approximately two orders of magnitude. We therefore expect that the embedded cluster approach will enable wider RPA implementation in heterogeneous catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Biological Electron Transfer and Catalysis EFRC

The focus of the Biological Electron Transfer and Catalysis (BETCy) EFRC research is elucidating mechanisms of conversion of electrochemical potential into chemical bond energy and is organized into two integrated Thrusts: Electron Bifurcation Catalysis and Electron Transfer Kinetics. We are developing a collective knowledge of metalloenzymes as models for redox reactions by applying physical science and computational tools to characterize biochemical reactions catalyzed by multi- subunit enzymes harboring arrays of iron-sulfur clusters and flavin cofactors. Understanding these mechanisms is central to overcoming the thermodynamic barriers that currently limit production of reduced products and fuels. Biological systems have elegant strategies for converting electrochemical potential energy into chemical bond energy (e.g., C-H, H-H, and N-H) stored in reduced compounds that can serve as advanced biofuels. One significant limitation for the production of highly reduced compounds is that their production in natural and industrial processes relies on low oxidation-reduction potential chemicals as feedstocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗

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↗

Bragg Coherent Diffraction Imaging for In Situ Studies in Electrocatalysis

Electrocatalysis is at the heart of a broad range of physicochemical applications that play an important role in the present and future of a sustainable economy. Among the myriad of different electrocatalysts used in this field, nanomaterials are of ubiquitous importance. An increased surface area/volume ratio compared to bulk makes nanoscale catalysts the preferred choice to perform electrocatalytic reactions. Bragg coherent diffraction imaging (BCDI) was introduced in 2006 and since has been applied to obtain 3D images of crystalline nanomaterials. BCDI provides information about the displacement field, which is directly related to strain. Lattice strain in the catalysts impacts their electronic configuration and, consequently, their binding energy with reaction intermediates. Even though there have been significant improvements since its birth, the fact that the experiments can only be performed at synchrotron facilities and its relatively low resolution to date (~10 nm spatial resolution) have prevented the popularization of this technique. Herein, we will briefly describe the fundamentals of the technique, including the electrocatalysis relevant information that we can extract from it. Subsequently, we review some of the computational experiments that complement the BCDI data for enhanced information extraction and improved understanding of the underlying nanoscale electrocatalytic processes. We next highlight success stories of BCDI applied to different electrochemical systems and in heterogeneous catalysis to show how the technique can contribute to future studies in electrocatalysis. Finally, we outline current challenges in spatiotemporal resolution limits of BCDI and provide our perspectives on recent developments in synchrotron facilities as well as the role of machine learning and artificial intelligence in addressing them.

bragg coherent diffraction imaging↗

Binding of Formic Acid on Anatase TiO2(101)

The adsorption of formic acid (FA) and the formation of formate species on metal oxide surfaces are of great interest in catalysis. Formic acid is used to probe the adsorption properties of surface sites and formates are common intermediates in many catalytic reactions. Here we focus on the interaction of FA with a prototypical anatase TiO2(101) surface by using a combination of scanning tunneling microscopy (STM), infrared reflection absorption spectroscopy (IRAS), electron stimulated desorption (ESD), and density functional theory (DFT) to assess the coverage dependent evolution of different FA-derived surface species at low temperatures (80–240 K). We find that isolated FA adsorbs at 80 K in both monodentate (MD) and bidentate (BD) configurations on top of undercoordinated Ti sites (Ti5c). The MD form is likely deprotonated and readily converts upon annealing to bridging BD on two neighboring Ti5c sites. DFT calculations show that molecularly-bound MD FA is metastable and readily converts into a deprotonated state in the proximity of subsurface oxygen vacancy. The stability of the MD species increases as the availability of the paired Ti5c sites for BD formation diminishes at high coverages. Upon surface saturation, a mixed configuration of alternating bidentate and monodentate species with coverage of 2/3 FA/Ti5c represents the most favorable configuration. This is in contrast with the adsorption of FA on rutile TiO2(110) and many other oxides, where bidentate formate species dominate. Y.W., A.D., G.A.K., R.R., N.G.P., and Z.D. were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences and Biosciences (CSGB) under FWP 47319. B.W. and A.S. acknowledge the support of DOE BES, CSGB Division under Award DESC0007347. The experimental studies were performed in EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated for DOE by Battelle. The authors also acknowledge computational resources from the TIGRESS high-performance computer center at Princeton University.

Wang, Yang↗

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.↗

Synthetic and Mechanistic Implications of Chlorine Photoelimination in Nickel/Photoredox C(sp 3 )–H Cross-Coupling

In recent years, the development of light-driven reactions has contributed numerous advances in synthetic organic chemistry. A particularly active research area combines photoredox catalysis with nickel catalysis to accomplish otherwise inaccessible cross-coupling reactions. In these reactions, the photoredox catalyst absorbs light to generate an electronically excited charge-transfer state that can engage in electron or energy transfer with a substrate and the nickel catalyst. Our group questioned whether photoinduced activation of the nickel catalyst itself could also contribute new approaches to cross-coupling. Over the past 5 years, we have sought to advance this hypothesis for the development of a suite of mild and site-selective C(sp 3 )–H cross-coupling reactions with chloride-containing coupling partners via photoelimination of a Ni–Cl bond. On the basis of a report from the Nocera laboratory, we reasoned that photolysis of a Ni(III) aryl chloride species, generated by single-electron oxidation of a typical Ni(II) intermediate in cross-coupling, might allow for the catalytic generation of chlorine atoms. Combining this with the ability of Ni(II) to accept alkyl radicals, we hypothesized that photocatalytically generated chlorine atoms could mediate hydrogen atom transfer (HAT) with C(sp 3 )–H bonds to generate a substrate-derived alkyl radical that is captured by the Ni center in cross-coupling. A photoredox catalyst was envisioned to promote the necessary single-electron oxidation and reduction of the Ni catalyst to facilitate an overall redox-neutral process. Overall, this strategy would offer a visible-light-driven mechanism for chlorine radical formation enabled by the sequential capture of two photons. As an initial demonstration, we developed a Ni/photoredox-catalyzed α-oxy C(sp 3 )–H arylation of cyclic and acyclic ethers. This method was extended to a mild formylation of abundant and complex aryl chlorides through selective 2-functionalization of 1,3-dioxolane. Seeking to develop a suite of reactions that introduce carbon at all different oxidation states, we explored C(sp 3 )–H cross-coupling with trimethyl orthoformate, a common laboratory solvent. We found that trimethyl orthoformate serves as a source of methyl radical for a methylation reaction via β-scission from a tertiary radical generated upon chlorine-mediated HAT. Since chlorine radical is capable of abstracting unactivated C(sp 3 )–H bonds, our efforts have also been directed at cross-coupling with a range of feedstock chemicals, such as alkanes and toluenes, along with late-stage intermediates, using chloroformates as coupling partners. Overall, this platform enables access to valuable synthetic transformations with (hetero)aryl chlorides, which despite being the most ubiquitous and inexpensive aryl halide coupling partners, are rarely reactive in Ni/photoredox catalysis. Little is known about the photophysics and photochemistry of organometallic Ni complexes relevant to cross-coupling. We have conducted mechanistic investigations, including computational, spectroscopic, emission quenching, and stoichiometric oxidation studies, of Ni(II) aryl halide complexes common to Ni/photoredox reactions. These studies indicate that chlorine radical generation from excited Ni(III) is operative in the described C(sp 3 )–H functionalization methods. More generally, the studies illustrate that the photochemistry of cross-coupling catalysts cannot be ignored in metallaphotoredox reactions. We anticipate that further mechanistic understanding should facilitate catalyst design and lead to the development of new synthetic methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗

Hydrogen in Nanocatalysis

Hydrogen is ubiquitous in catalysis. It is involved in many important reactions such as water splitting, N 2 reduction, CO 2 reduction, and alkane activation. In this Perspective, we focus on the hydrogen atom and follow its electron as it interacts with a catalyst or behaves as part of a catalyst from a computational point of view. In this work, we present recent examples in both nanocluster and solid catalysts to elucidate the parameters governing the strength of the hydrogen–surface interactions based on site geometry and electronic structure. We further show the interesting behavior of hydride in nanometal and oxides for catalysis. Overall, the key take-home messages are: (1) the in-the-middle electronegativity and small size of hydrogen give it great versatility in interacting with active sites on nanoparticles and solid surfaces; (2) the strength of hydrogen binding to an active site on a surface is an important descriptor of the chemical and catalytic properties of the surface; (3) the energetics of the hydrogen binding is closely related to the electronic structure of the catalyst; (4) hydrides in nanoclusters and oxides and on surfaces offer unique reactivity for reduction reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Advances in in situ/operando techniques for catalysis research: enhancing insights and discoveries

Abstract Catalysis research has witnessed remarkable progress with the advent of in situ and operando techniques. These methods enable the study of catalysts under actual operating conditions, providing unprecedented insights into catalytic mechanisms and dynamic catalyst behavior. This review discusses key in situ techniques and their applications in catalysis research. Advances in in situ electron microscopy allow direct visualization of catalysts at the atomic scale under reaction conditions. In situ spectroscopy techniques like X-ray absorption spectroscopy and nuclear magnetic resonance spectroscopy can track chemical states and reveal transient intermediates. Synchrotron-based techniques offer enhanced capabilities for in situ studies. The integration of in situ methods with machine learning and computational modeling provides a powerful approach to accelerate catalyst optimization. However, challenges remain regarding radiation damage, instrumentation limitations, and data interpretation. Overall, continued development of multi-modal in situ techniques is pivotal for addressing emerging challenges and opportunities in catalysis research and technology.

Chen, Linfeng↗

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↗

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.↗

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.↗

Graph theory approach to determine configurations of multidentate and high coverage adsorbates for heterogeneous catalysis

Abstract Heterogeneous catalysts constitute a crucial component of many industrial processes, and to gain an understanding of the atomic-scale features of such catalysts, ab initio density functional theory is widely employed. Recently, growing computational power has permitted the extension of such studies to complex reaction networks involving either high adsorbate coverages or multidentate adsorbates, which bind to the surface through multiple atoms. Describing all possible adsorbate configurations for such systems, however, is often not possible based on chemical intuition alone. To systematically treat such complexities, we present a generalized Python-based graph theory approach to convert atomic scale models into undirected graph representations. These representations, when combined with workflows such as evolutionary algorithms, can systematically generate high coverage adsorbate models and classify unique minimum energy multidentate adsorbate configurations for surfaces of low symmetry, including multi-elemental alloy surfaces, steps, and kinks. Two case studies are presented which demonstrate these capabilities; first, an analysis of a coverage-dependent phase diagram of absorbate NO on the Pt 3 Sn(111) terrace surface, and second, an investigation of adsorption energies, together with identifying unique minimum energy configurations, for the reaction intermediate propyne (CHCCH 3 *) adsorbed on a PdIn(021) step surface. The evolutionary algorithm approach reproduces high coverage configurations of NO on Pt 3 Sn(111) using only 15% of the number of simulations required for a brute force approach. Furthermore, the screening of potentially hundreds of multidentate adsorbates is shown to be possible without human intervention. The strategy presented is quite general and can be applied to a spectrum of complex atomic systems.

36 MATERIALS SCIENCE↗

Machine learning-assisted crystal engineering of a zeolite

Abstract It is shown that Machine Learning (ML) algorithms can usefully capture the effect of crystallization composition and conditions (inputs) on key microstructural characteristics (outputs) of faujasite type zeolites (structure types FAU, EMT, and their intergrowths), which are widely used zeolite catalysts and adsorbents. The utility of ML (in particular, Geometric Harmonics) toward learning input-output relationships of interest is demonstrated, and a comparison with Neural Networks and Gaussian Process Regression, as alternative approaches, is provided. Through ML, synthesis conditions were identified to enhance the Si/Al ratio of high purity FAU zeolite to the hitherto highest level (i.e., Si/Al = 3.5) achieved via direct (not seeded), and organic structure-directing-agent-free synthesis from sodium aluminosilicate sols. The analysis of the ML algorithms’ results offers the insight that reduced Na 2 O content is key to formulating FAU materials with high Si/Al ratio. An acid catalyst prepared by partial ion exchange of the high-Si/Al-ratio FAU (Si/Al = 3.5) exhibits improved proton reactivity (as well as specific activity, per unit mass of catalyst) in propane cracking and dehydrogenation compared to the catalyst prepared from the previously reported highest Si/Al ratio (Si/Al = 2.8).

36 MATERIALS SCIENCE↗

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.↗

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.↗