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Rodriguez, Jose A.

Publications and source records attributed to Rodriguez, Jose A..

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Accounting for electron-beam-induced warping of molecular nanocrystals in MicroED structure determination

High-energy electrons induce sample damage and motion at the nanoscale to fundamentally limit the determination of molecular structures by electron diffraction. Using a fast event-based electron counting (EBEC) detector, we characterize beam-induced, dynamic, molecular crystal lattice reorientations (BIRs). These changes are sufficiently large to bring reciprocal lattice points entirely in or out of intersection with the sphere of reflection, occur as early events in the decay of diffracted signal due to radiolytic damage, and coincide with beam-induced migrations of crystal bend contours within the same fluence regime and at the same illuminated location on a crystal. These effects are observed in crystals of biotin, a series of amino acid metal chelates, and a six-residue peptide, suggesting that incident electrons inevitably warp molecular lattices. The precise orientation changes experienced by a given microcrystal are unpredictable but are measurable by indexing individual diffraction patterns during beam-induced decay. Reorientations can often tilt a crystal lattice several degrees away from its initial position before irradiation, and for an especially beam-sensitive Zn(II)-methionine chelate, are associated with dramatic crystal quakes prior to 1 e − Å −2 electron beam fluence accumulates. Since BIR coincides with the early stages of beam-induced damage, it echoes the beam-induced motion observed in single-particle cryoEM. As with motion correction for cryoEM imaging experiments, accounting for BIR-induced errors during data processing could improve the accuracy of MicroED data.

Vlahakis, Niko (ORCID:0000000250920265)↗
DOE OSTI2024

Mapping Electron Beam-Induced Radiolytic Damage in Molecular Crystals

Every electron crystallography experiment is fundamentally constrained by radiation damage [1]. Despite its crucial importance, little is understood about the onset and progression of radiolysis in beam-sensitive molecular crystals [2]. Since the typical metric used for monitoring the degradation induced by radiolysis is the attenuation of Bragg reflections in electron diffraction patterns [3], the scope of previous analyses [2-6] has mostly been limited to indirect observation via the back focal plane. Here, a simultaneous visualization of the effects of electron beam-induced radiolysis—in both real space and reciprocal space—remains elusive.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

3D Nanocrystallography and the Imperfect Molecular Lattice

Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.

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

AlphaFold -assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography

Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.

molecular replacement↗
DOE OSTI2023

Beyond MicroED: Ab Initio Structure Elucidation using 4D-STEM

Microcrystal electron diffraction (microED) has recently morphed into an increasingly mainstream technique in structural chemistry [1]. Its ability to interrogate nanocrystals orders of magnitude too small for conventional X-ray diffraction has enabled solid-state structure elucidation of several species previously considered impossible to solve using X-ray crystallography [2, 3]. Furthermore, selected area aperture-enabled microED remains thwarted by the presence of disordered, overlapping, or otherwise poorly diffracting domains, all of which routinely conspire to diminish data quality. Just as insufficient crystal size historically stymied conventional X-ray methods, these nanoscale defects frequently prohibit structure solution using classical microED.

Saha, Ambarneil↗
DOE OSTI2023

The α-WC(0001) Surface as a Hydrogen Sponge: A First Principle Study of H 2 Dissociation and Formation of Low and High Coverages

Tungsten carbide (WC) displays a Pt-like behavior in catalysis, applied in hydrogenation processes. Numerous theoretical studies have modeled the behavior and use of adsorbed hydrogen without obtaining a general picture, missing basic links between H 2 dissociation and generation of high surface coverage (Θ H >0.5 ML). Here, in this study, the capability of C- and W-terminations of the α-WC(0001) surface is analyzed to dissociate several H 2 molecules to produce coverages, Θ H , ranging from low to very high values (0.13<Θ H <2.00 ML). Density functional theory and an ab initio atomistic thermodynamic were used to achieve the conditions for H 2 dissociation. The WC–C surface has higher capacity to dissociate H 2 molecules than WC–W. However, both surfaces can reach full surface coverage, Θ H =1 ML, at mild ambient conditions, T=300 K and P=1 atm, and even up to 500 K at low and high pressures. The H-adatoms on WC–W are more labile than on WC–C. The binding of adsorbates is hindered at high Θ H , implying a need to modulate Θ H according to the application. The results give the basis to understand the capabilities of WC-based catalysts in hydrogenation-related reactions, with the advantage of WC being a hydrogen reservoir at mild practical catalytic conditions.

03 NATURAL GAS↗
DOE OSTI2022

Investigating the Elusive Nature of Atomic O from CO 2 Dissociation on Pd(111): The Role of Surface Hydrogen

CO 2 dissociation is a key step in CO 2 conversion reactions to produce value-added chemicals typically through hydrogenation. In many cases, the atomic O produced from CO 2 dissociation can potentially block adsorption sites or change the oxidation state of the catalyst. Here, we used ambient pressure X-ray photoelectron spectroscopy (AP-XPS) and density functional theory (DFT) calculations to investigate the presence of surface species from the dissociation of CO 2 on Pd(111). AP-XPS results show that CO 2 was dissociated to produce adsorbed CO, but dissociated atomic O was not observed at room temperature. We were only able to observe atomic O when CO 2 was introduced at 500 K. Further investigations of O-covered Pd(111) revealed that chemisorbed O could be easily removed by low pressures of CO and H 2 . Notably, the effect of H 2 is quite prominent since it could react with chemisorbed O at a pressure as low as 2 × 10 -9 Torr, and the presence of H2 at ambient pressure prevented CO 2 dissociation. DFT calculations showed that in the presence of background H 2 , facile CO 2 dissociation took place via the reverse water–gas shift (rWGS) reaction, which resulted in the formation of adsorbed CO and removal of O by H 2 . DFT also identified the possible variation of surface species on simultaneous exposure of CO 2 and H 2 over Pd(111) depending on temperature and pressure, which opens alternative opportunities to tune the CO 2 hydrogenation catalysis by controlling the reaction conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Au and Pt Remain Unoxidized on a CeO 2 -Based Catalyst during the Water–Gas Shift Reaction

The active form of Au and Pt in CeO 2 based catalysts for the WGS reaction is an issue that although it has been widely studied remains unclear. On one hand, ionic species might be responsible of weakening the Ce-O bonds increasing the oxygen mobility and WGS activity. On the other hand, the close contact of Au or Pt atoms with CeO 2 oxygen vacancies at the metal/CeO 2 interface might provide the active sites for an efficient reaction. In this work, by using in-situ X-ray absorption spectroscopy, we demonstrate that both Au and Pt remain unoxidized during the reaction. Here, remarkable differences involving the dynamics established by both species under WGS atmospheres were recognized. For the pre-reduced Pt catalyst, an increase of the conversion coincided with a re-structuration of the Pt atoms into cuboctahedrical metallic particles without significant variations on the overall particle size. Contrary to the relatively static behavior of Pt 0 , Au 0 nanoparticles exhibited a sequence of particle splitting and agglomeration whilst maintaining a zero oxidation state, even though not being located in a metallic environment during the process. High WGS activity was obtained when Au atoms were surrounded by oxygen. The fact that Au preserves its unoxidized state indicates that the chemical interaction between Au and oxygen must be necessarily electrostatic being such electrostatic interaction fundamental for a top performance in the WGS process.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Infrared reflection absorption spectroscopy and temperature-programmed desorption studies of CO adsorption on Ni/CeO 2 (111) thin films: The role of the ceria support

Ceria-supported Ni has shown unique catalytic activity due to unique properties of small Ni particles and strong metal-support interaction. Identification of adsorption sites and understanding the chemical interaction over Ni-ceria at the fundamental level provide crucial insights into the reaction pathways of complex catalytic processes. In this study, to probe the surface sites, the adsorption of CO was carried out with model Ni/ceria systems consisting of Ni nanoparticles vapor-deposited on well-ordered CeO x (111) (1.5 < x < 2) thin films using infrared reflection absorption spectroscopy (IRRAS) and temperature-programmed desorption (TPD) under ultrahigh vacuum (UHV) conditions. Fully oxidized CeO 2 (111) (Ce 4+ ) and partially reduced CeO 1.75 (111) (Ce 4+ /Ce 3+ ) thin films were grown on Ru(0001) to examine the role of the ceria support. Additionally, Ni with low coverages (e.g., 0.2 ML) grows forming small two-dimensional particles on ceria at 300 K, which develop into three-dimensional clusters after heating to 700 K. In the absence of Ni, CO adsorption at 1 mTorr at 100 K shows distinct IR bands at 2158 cm -1 on CeO 2 and 2165 cm -1 on CeO 1.75 . Bridging and atop IR bands associated with CO adsorption over metallic Ni were observed on the Ni-CeO 1.75 surface at 300 K under UHV conditions. CO adsorption over Ni 0 was also observed over as-deposited Ni on CeO 2 . However, a new IR band at 2146 cm -1 due to CO adsorption over Ni 2+ species was detected at 100 K over the annealed Ni particles on CeO 2 . CO IRRAS data suggest the oxidation of Ni to Ni 2+ on CeO 2 and the formation of predominant Ni 2+ species with heating, which is further confirmed with CO TPD data and previous x-ray photoelectron spectroscopy results.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Reversing sintering effect of Ni particles on γ-Mo 2 N via strong metal support interaction

Reversing the thermal induced sintering phenomenon and forming high temperature stable fine dispersed metallic centers with unique structural and electronic properties is one of the ever-lasting targets of heterogeneous catalysis. Here we report that the dispersion of metallic Ni particles into under-coordinated two-dimensional Ni clusters over γ-Mo 2 N is a thermodynamically favorable process based on the AIMD simulation. A Ni-4nm/γ-Mo 2 N model catalyst is synthesized and used to further study the reverse sintering effect by the combination of multiple in-situ characterization methods, including in-situ quick XANES and EXAFS, ambient pressure XPS and environmental SE/STEM etc. The under-coordinated two-dimensional layered Ni clusters on molybdenum nitride support generated from the Ni-4nm/γ-Mo 2 N has been demonstrated to be a thermally stable catalyst in 50 h stability test in CO 2 hydrogenation, and exhibits a remarkable catalytic selectivity reverse compared with traditional Ni particles-based catalyst, leading to a chemo-specific CO 2 hydrogenation to CO.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Size and Stoichiometry Effects on the Reactivity of MoCy Nanoparticles Towards Ethylene

Molybdenum carbides are promising catalysts alternative to Pt-group metals for the hydrogenation of unsaturated hydrocarbons. Nanostructuring has been shown to be an efficient way to boost the catalytic activity of these materials with MoCy nanoparticles (NPs) exhibiting a good performance when encapsulated inside zeolites or dispersed on inert supports such as carbon or gold. In this work, we focus on a systematic DFT study of the interaction of MoCy NPs with ethylene (C 2 H 4 ), as a general and simple approach for examining binding and activation of C≡C bonds. Models for 14 NPs, with a Mo/C ratio in the 0.67 to 2.00 range, have been built following a cascade procedure. Several chemical descriptors, including the adsorption energy, structural NPs distortion, C≡C deformation, and C 2 H 4 attachment energy have been analyzed along with a meticulous geometric and electronic characterization of bare NPs and C2H4 binding. The present results show that 1:1 stoichiometric Mo 6 C 6 , Mo 12 C 12 , and Mo 24 C 24 , and the non-stochiometric Mo 4 C 6 , Mo 8 C 12 (MetCar), and Mo 14 C 13 (Nanocube) are excellent systems for the binding and activation of ethylene, exhibiting a much bigger reactivity than a bulk δ-MoC(001) surface with a similar Mo:C ratio. In addition, C 2 H 4 binding on the NPs with a Mo/C < 1.08 is advantageous since, apart from a rather large adsorption energy, implies low energy values for NPs deformation (from 0.00 to 0.31 eV), C≡C distortion (from 0.30 to 0.52 eV), and C 2 H 4 attachment (from -2.12 to -2.58 eV). These theoretical results point to the ideal MoCy size and composition for C 2 H 4 binding, providing a background for further experimental studies aimed at the preparation of MoCy NPs as hydrogenation catalysts.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Modulation of the Effective Metal-Support Interactions for the Selectivity of Ceria Supported Noble Metal Nanoclusters in Atmospheric CO 2 Hydrogenation

Ever-increasing attention is given to the sustainable utilization of CO 2 in the atmosphere out of environmental and economic considerations. The deep-going clarification of the effective and ineffective metal-support interactions (MSI) in the supported catalysts for the catalytic performance of CO 2 hydrogenation is particularly needed to design highly active nanocatalysts. How to tune the MSI to be effective for the selectivity of goal hydrogenation products is a significant but rather challenging subject. In this work, we demonstrate that the selectivity in CO 2 hydrogenation can be regulated from preferential CH 4 production to preferential CO production by varying the nature of the electronic MSI for ceria supported noble metal nanoclusters, and the effective MSI play a pivotal role for the catalytic systems with opposite hydrogenation selectivity. The modulation of the effective MSI for the selectivity in CO 2 hydrogenation sheds new light on the comprehensive understanding of the MSI and interfacial effects in terms of tailoring and controlling the performance of supported heterogeneous catalysts.

36 MATERIALS SCIENCE↗