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At least 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Surface Protection and Catalytic CH Alumination

This dataset supports a publication, "Surface Protected Organozirconium Catalyzes C–H Alumination of Saturated Hydrocarbons", and describes the surface-organozirconium catalyzed exchange of ethyl group in AlEt3 for dodecyl or methyl from dodecane or methane. The research describes the benefits of capping remaining surface OH with SiMe3 for improving yields and turnovers. The dataset includes characterization of the precatalyst using solid-state nuclear magnetic resonance spectroscopy and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), as well as gas chromatography and solution NMR of reaction products.

Catalysis and mechanisms of reactions↗
DOE OSTI2020

IDENTIFICATION OF ADSORBA TION OF ADSORBATE FT-IR BANDS USING IN-SI -IR BANDS USING IN-SITU TECHNIQUES: Pd SPECIATION AND ADSORPTION CHEMISTRY OF Pd-ZEOLITES FOR PASSIVE NOx ADSORPTION

To meet increasingly stringent automotive emissions standards, further improvements in catalytic converter design are necessary. Current automotive catalyst systems are effective at eliminating emission of nitrogen oxides (NOx) once the catalyst reaches operational temperature (~200 °C). NOx emitted at lower catalyst temperatures now comprises most of the NOx released during a typical test cycle. Referred to as “the cold start problem” this issue has come to the forefront of automotive catalyst development, as mitigating these emissions is necessary to further reduce automotive emissions. Passive NOx adsorbers present an appealing solution to the cold start problem, these being a class of materials that chemisorb exhaust components such as NOx, carbon monoxide (CO) and hydrocarbons at near-ambient temperatures, and then desorb these compounds once the downstream catalyst has reached operational temperature. An effective passive NOx adsorber must have several properties: high NOx adsorption at near-ambient temperatures, near-complete NOx desorption at temperatures within the operational range, high thermal stability, and resistance to automotive exhaust components at high temperatures. The potential environmental impact of such a system is substantial, as NOx emissions currently result in the formation of millions of tons of smog and acid rain each year. Pd-exchanged zeolites have shown promise for deployment as Passive NOx adsorbers, though much remains to be understood about their adsorption chemistry and deactivation. In-situ Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) provides a convenient probe of adsorbed species, most automotive exhaust components possessing IR-active chemical bonds. By examining the evolution of IR bands under various pretreatments and adsorbates, the overall Pd-speciation and adsorptive zeolite sites of each material can be characterized, and the identities of IR bands can be deduced. In this work, microreactor-MS analysis of the adsorption and desorption behavior of these materials was also examined, these results being coupled with in-situ DRIFTS temperature programmed desorption (TPD) to correlate desorption events with specific adsorbed species. A pair of zeolite frameworks of similar Si/Al ratio but differing pore size were examined, Beta zeolite (BEA) and Chabazite (CHA) representing a medium- and small-pore framework, respectively. The effect of Pd-loading on BEA was examined, as well as the various deactivation pathways and active sites of each material.

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

Copper Reductase Activity and Free Radical Chemistry by Cataract-Associated Human Lens γ-Crystallins

Cataracts are caused by high-molecular weight aggregates of human eye lens proteins that scatter light, causing lens opacity. Metal ions have emerged as important potential players in the etiology of cataract disease, as human lens γ-crystallins are susceptible to metal-induced aggregation. Here, the interaction of Cu 2+ ions with γD-, γC-, and γS- crystallins, the three most abundant γ-crystallins in the lens, has been evaluated. Cu 2+ ions induced non-amyloid aggregation in all three proteins. Solution turbidimetry, SDS-PAGE, circular dichroism and differential scanning calorimetry showed that the mechanism for Cu-induced aggregation involves: i) loss of beta-sheet structure in the N-terminal domain; ii) decreased thermal and kinetic stability; iii) formation of metal-bridged species; and iv) formation of disulfide-bridged dimers. Electron paramagnetic resonance (EPR) revealed two distinct Cu 2+ binding sites in each protein. Spin quantitation demonstrated reduction of γ-crystallin-bound Cu 2+ ions to Cu + under aerobic conditions, while X-ray absorption spectroscopy (XAS) confirmed the presence of linear or trigonal Cu + binding sites in γ-crystallins. Our EPR and XAS studies revealed that γ-crystallins’ Cu 2+ reductase activity yields a protein-based free radical that is likely a Tyr-based species in human γD-crystallin. This unique free radical chemistry carried out by distinct redox-active Cu sites in human lens γ-crystallins likely contributes to the mechanism of copper-induced aggregation. Finally, in the context of an aging human lens, γ-crystallins could be acting, not only as structural proteins, but also as key players for metal and redox homeostasis.

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

Runtime performance of a GAMESS quantum chemistry application offloaded to GPUs

Summary Computational chemistry is at the forefront of solving urgent societal problems, such as polymer upcycling and carbon capture. The complexity of modeling these processes at appropriate length and time scales is mainly manifested in the number and types of chemical species involved in the reactions and may require models of several thousand atoms and large basis sets to accurately capture the chemical complexity and heterogeneity in the physical and chemical processes. The quantum chemistry package General Atomic and Molecular Electronic Structure System (GAMESS) has a wide array of methods that can efficiently and accurately treat complex chemical systems. In this work, we have used the GAMESS Effective Fragment Molecule Orbital (EFMO) method for electronic structure calculation of a challenging mesoporous silica nanoparticle (MSN) model surrounded by about 4700 water molecules to investigate the strong scaling and GPU offloading on hybrid CPU‐GPU nodes. Experiments were performed on the Perlmutter platform at the National Energy Research Scientific Computing Center. Good strong scaling and load balancing have been observed on up to 88 hybrid nodes for different settings of the execution parameters for the calculation considered here. When GPUs are oversubscribed by offloading work from multiple CPU processes, using the NVIDIA multi‐process service (MPS) has consistently reduced time to solution and energy consumed. Additionally, for some configuration parameter settings, oversubscription with MPS improved performance by up to 5.8% over the case without oversubscription.

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

ORNL_AISD_NiNb

This dataset describes the nickel-niobium solid solution binary alloy, where the two constituent elements nickel (Ni) and niobium (Nb) are randomly placed on an underlying crystal lattice. This dataset for nickel-niobium (Ni-Nb) alloys available includes the formation energy and bulk modulus for each crystal structure. Each atomic sample has a disordered phase which is obtained starting from an initial regular crystal structure of type body-centered cubic (BCC), face-centered cubic (FCC), or hexagonal compact packed (HCP). The geometry optimization ensures that all the alloy samples reached the equilibrium with negative formation energy. We perform geometry optimizations using the LAMMPS simulation package [1], a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. We utilized the embedded atom model (EAM) potential for Ni and Nb developed in a previous study [2]. The potential could describe behaviors of the liquid and solid phases of Ni-Nb alloy. The structural factors and angular distributions of three atoms are well-matched with X-ray and ab initio-based molecular dynamics data. We prepared the three different crystals with different initial lattice parameters (3.52 Ã… for FCC, 3.32 Ã… for BCC, and 3.5 Ã… for HCP). We performed energy minimization in two steps. Firstly, we minimized the structures with an isotropic unit cell to minimize the side effects from our arbitrary lattice parameters for all other compositions. Then, we applied geometry optimization with a triclinic (non-orthogonal) unit cell to fully minimize the stress components to calculate the elastic constants. In this procedure, we chose 10,000 as the maximum number of allowable steps aimed at obtaining fully relaxed atomic geometries. The dataset consists of three sets of crystal structures. The first set contains 46,086 irregular crystal structures, each of them with 54 atoms, obtained through optimization starting from a regular BCC crystal structure. The second set contains 24,543 irregular crystal structures, each of them with 32 atoms, obtained through optimization starting from a regular FCC crystal structure. The third set contains 39,303 irregular crystal structures, each of them with 48 atoms, obtained through optimization starting from a regular HCP crystal structure. The atomic configurations within each set span the possible compositional range. The three sets have been unified in a global dataset, which is extremely heterogeneous in terms of crystal structures, lattice volumes, and atomic configurations. Organization of files inside the dataset: the dataset contains three subdirectories called • BCC_opt • FCC_opt • HCP_opt based on the type of initial regular structure used to start the geometry optimization. Inside each of these folders, every atomic structure is identified by a string “A_B_Câ€, where A denotes the number of Nb in the system, B denotes index of structure with a given Nb number, and C denotes the total number of structures generated with a given Nb number. For each optimized crystal structure identified by the unique string of characters “A_B_Câ€, three files are provided: • A_B_C_opt.xyz: The optimized geometries in xyz format • A_B_C_opt.cfg: The optimized geometries in cfg format. It includes cell information and atomic energy, and forces calculated from LAMMPS. • A_B_C.elastic: Raw data of 21 elastic constants from LAMMPS output. • A_B_C.bulk: Calculated upper and lower bounds of bulk modulus and averaged one based on Voigt-Reuss-Hill approach from *.elastic. References: [1] A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, and S. J. Plimpton. LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comp. Phys. Comm., 271:108171, 2022. [2] Y Zhang, R Ashcraft, MI Mendelev, CZ Wang, and KF Kelton. Experimental and molecular dynamics simulation study of structure of liquid and amorphous ni62nb38 alloy. The Journal of chemical physics, 145(20):204505, 2016.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Chemical Functional Groups Regulate Ion Concentrations and pHs in Nanopores

Understanding ion behaviors in functionalized nanopores is essential to deciphering reactions in both natural and engineered systems, such as sediments, biological ion channels, and membranes. While many efforts have shown the modified ion behaviors in the functionalized nanopores, a direct measurement and analysis to show how chemical functional groups affect ion concentrations in nanopores are critically needed. In this work, we present a plasmonic nanosensor that can measure the local concentrations of protons, anions (phosphate, nitrate, sulfate, and arsenate), and cations (mercury, lead, and copper) in functionalized nanopores, and we compare their concentrations in nanopores with the corresponding bulk concentrations. Notably, chemical functional groups induced ion concentrations differently in nanopores. In pristine nanopores and methyl- and phenyl-functionalized nanopores, we discovered an unexpected concurrence of an enhanced anion concentration and a suppressed cation concentration. In addition, the nanopore pH is dependent on bulk solution compositions and can be lower by 2.5 units, even when the bulk solution is well-buffered. In contrast, for hydrophilic (amine, thiol, and carboxyl) nanopores, pH depended on the p K a of the functional groups, and the heavy metal concentrations depended on chemical interactions with the functional groups. Our findings provide a better understanding of water chemistry in nanopores and can help precisely control ions in nanopores to benefit the design of membrane-based desalination techniques, CO 2 storage, and porous catalysts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Global Pathway Selection with Zero-RK

Global Pathway Selection (GPS) is an algorithm to effectively generates reduced (skeletal) chemistry mechanisms, which speeds up simulations and can be used as a systematic analytics tool to extract insights from complex reacting system. This release is an extension of the original code to run in parallel and to use LLNL's Zero-RK solver for fast solution of chemical problems.

Whitesides, RussellA↗
DOE OSTI2024

TChem-atm v1.0

SAND2024-11300O TChem-atm is a software library that was developed to solve complex kinetic models for atmospheric chemistry applications. TChem-atm interface employs a hierarchical parallelism design to exploit the massive parallelism available from modern computing platforms. It also supports gas atmospheric chemistry applications, e.g., the energy exascale earth system model. TChem can be used as a box model or coupled with a climate model to compute the time evolution of gas tracer species. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Safta, Cosmin↗
DOE OSTI2025

Global Pathway Selection with Zero-RK v0.5

Global Pathway Selection (GPS) is an algorithm to effectively generates reduced (skeletal) chemistry mechanisms, which speeds up simulations and can be used as a systematic analytics tool to extract insights from complex reacting system. This release is an extension of the original code to run in parallel and to use LLNL's Zero-RK solver for fast solution of chemical problems.

Whitesides, RussellA [Lawrence Livermore National ↗
DOE OSTI2022

Node Distortion as a Tunable Mechanism for Negative Thermal Expansion in Metal–Organic Frameworks

Chemically functionalized series of metal–organic frameworks (MOFs), with subtle differences in local structure but divergent properties, provide a valuable opportunity to explore how local chemistry can be coupled to long-range structure and functionality. Using in situ synchrotron X-ray total scattering, with powder diffraction and pair distribution function (PDF) analysis, we investigate the temperature dependence of the local- and long-range structure of MOFs based on NU-1000, in which Zr 6 O 8 nodes are coordinated by different capping ligands (H 2 O/OH, Cl – ions, formate, acetylacetonate, and hexafluoroacetylacetonate). We show that the local distortion of the Zr 6 nodes depends on the lability of the ligand and contributes to a negative thermal expansion (NTE) of the extended framework. Using multivariate data analyses, involving non-negative matrix factorization (NMF), we demonstrate a new mechanism for NTE: progressive increase in the population of a smaller, distorted node state with increasing temperature leads to global contraction of the framework. The transformation between discrete node states is noncooperative and not ordered within the lattice, i.e., a solid solution of regular and distorted nodes. Density functional theory calculations show that removal of ligands from the node can lead to distortions consistent with the Zr···Zr distances observed in the experiment PDF data. Control of the node distortion imparted by the nonlinker ligand in turn controls the NTE behavior. Furthermore, these results reveal a mechanism to control the dynamic structure of MOFs based on local chemistry.

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

The Role of Interfaces and Charge for Chemical Reactivity in Microdroplets

A wide variety of reactions are reported to be dramatically accelerated in aqueous microdroplets, making them a promising platform for environmentally clean chemical synthesis. However, to fully utilize the microdroplets for accelerating chemical reactions requires a fundamental understanding of how microdroplet chemistry differs from that of a homogeneous phase. Here, in this work, we provide our perspective on recent progress to this end, both experimentally and theoretically. We begin by reviewing the many ways in which microdroplets can be prepared, creating water/hydrophobic interfaces that have been frequently implicated in microdroplet reactivity due to preferential surface adsorption of solutes, persistent electric fields, and their acidity or basicity. These features of the interface interplay with specific mechanisms proposed for microdroplet reactivity, including partial solvation, possible gas phase channels, and the presence of highly reactive intermediates. We especially highlight the role of droplet charge and associated electric fields, which appears to be key to understanding how certain reactions, like the formation of hydrogen peroxide and reduced transition metal complexes, are thermodynamically possible in microdroplets. Lastly, we emphasize opportunities for theoretical advances and suggest experiments that would greatly enhance our understanding of this fascinating subject.

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

Bimetallic Copper/Ruthenium/Osmium Complexes: Observation of Conformational Differences Between the Solution Phase and Solid State by Atomic Pair Distribution Function Analysis

High-energy X-ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long-range order, but is underutilized for molecular complexes in solution. Here we demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic Cu I /Ru II /Os II complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal...metal distances separated by over 12 Å. The metal…metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub-Ångström conformational differences by direct comparison of solution phase and solid-state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules.

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

Experimental evaluation of the role of redox during glauconite-CO 2 -brine interactions

Greensands formations are globally abundant sedimentary rocks rich in Fe clays (typically glauconite) that commonly contain natural hydrocarbon accumulations and may be important reservoirs for geologic storage of anthropogenic CO 2 . Diagenesis in greensands is commonly accompanied by the conversion of primary glauconite to siderite (FeCO 3 ), a process that could be exploited for the permanent trapping of CO 2 . Importantly, siderite formation after glauconite requires that the mostly oxidized Fe in the primary Fe clay minerals is reduced during diagenetic interactions. Here, we explore the effect of solution redox state on the stability of glauconite in sandstones with implications for the diagenetic and/or engineered formation of siderite. We performed two flow-through experiments on intact, glauconite-rich sandstone cores at 150 °C and 150 bar. Both experiments employed a 1 mol NaCl/kg, 0.1 mol NaHCO 3 /kg solution charged with ~0.58 mol CO 2 /kg solution, but the redox state of the injected fluid was manipulated between experiments in order to compare glauconite reactivity and siderite saturation state at oxidizing and reducing end-member conditions. After reaction with the oxidizing (O 2 (aq) ≈ 6 μmol/kg) fluid, chemical and Mӧssbauer spectroscopic analyses indicate the production of Fe(III)-oxy/hydroxide minerals from glauconite, whereas, in the reducing (H 2 (aq) ≈ 5–40 mmol/kg) experiment, thermodynamic calculations and coupled chemical, mineralogical, and Mӧssbauer analyses suggest glauconite dissolution and precipitation of an Fe(II) mineral, likely siderite, and minor magnetite formation. These experimental results, along with thermodynamic calculations, confirm that solution redox state is the master variable dictating siderite formation in greensands.

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

Integrated membrane material design and system synthesis

In designing membrane systems, the synergy between membrane materials and the process design is often overlooked. In this paper, we present a mixed-integer nonlinear programming (MINLP) model for synthesizing membrane systems while simultaneously designing the respective membrane materials for multicomponent gas separation. The approach considers superstructure representations for systems with: (1) same, (2) potentially different, and (3) property-targeting membrane materials. In the first two systems, the selection of membrane material is a decision, while in the final type, membrane permeances are subject to optimization. Physics-based surrogate models are used to describe permeation in crossflow and countercurrent flow permeators. We show that, through a case study of biogas upgrading, our approach obtains high quality solutions. Furthermore, we use the proposed approach while considering permeance-based production cost to find the optimal membrane.

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

Frhodo: A program for simulating chemical kinetic measurements and optimizing kinetic mechanisms

Chemical kinetic simulations are frequently used to extract kinetic and mechanistic information from experimental data by fitting simulations to the data. For simple systems of consecutive single channel reactions this is a relatively straightforward task. However, as the complexity of the system increases and particularly for systems involving competitive multi-channel reactions manually optimizing a mechanism to obtain the best fits to a range of experimental data quickly becomes a time-intensive and challenging process, especially when rate coefficients have pressure and temperature dependencies. There is considerable potential for exploiting automated optimization methods to rapidly screen reaction mechanisms and optimize the fit by adjusting rate coefficients within well-defined constraints. A new chemical kinetics simulation program, Frhodo, has been developed for this purpose. The program allows either manual simulation of individual experiments or fully automated optimization against a range of experimental data by adjusting user selected reactions within user defined constraints. Frhodo incorporates machine learning-based optimization routines that work by either minimizing standardized residuals or through Bayesian parameter estimation. Frhodo's optimization capabilities are demonstrated by reexamining two previously studied systems of relevance to combustion. Dissociation of diacetyl followed by recombination of methyl radicals is an example of a sequence of single channel, consecutive reactions. Pyrolysis of 2-methyl furan exemplifies multi-channel, unimolecular reactions that are often encountered and have temperature and pressure dependencies in the rate coefficients of the channels and branching ratios between them. For both systems the optimization routines resulted in solutions similar to the original studies. Finally, comments are made on the strengths and limitations of the approach.

0D simulation↗