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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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63 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Unexpected Kinetic Solvent Effects Enhance Activity and Selectivity in Biphasic Systems

Biphasic dehydration of fructose to 5-hydroxymethylfurfural (HMF) has shown unprecedented increases in productivity, but a mechanistic understanding is lacking. Herein, we couple fast experimental reaction kinetics, multiscale modeling (phase behavior, classical molecular dynamics(MD), and quantum mechanics/molecular mechanics MD), in situ sampling, and IR and 13 C-NMR spectroscopy to elucidate the complex effects of nonpolar extracting organic solvents on the kinetics of fructose dehydration. We show that these organic solvents can reach significant mutual solubility with water at reaction temperatures, enabling the partition of the sugar and catalyst into the extracting phase. In the organic-rich environment, the dehydration of fructose proceeds faster and more selectively than in water due to increased relative abundance of the reactive furanose isomer, enhanced water–catalyst–substrate interactions driven by nanophase separation, and higher product stability stemming from preferential solvation. Furthermore, we demonstrate that these solvent effects impact other critical biphasic reactions in biomass upgrading and provide qualitative principles for solvent selection.

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

Liquid-Phase Effects on Adsorption Processes in Heterogeneous Catalysis

Aqueous solvation free energies of adsorption have recently been measured for phenol adsorption on Pt(111). Endergonic solvent effects of ~1 eV suggest solvents dramatically influence a metal catalyst’s activity with significant implications for the catalyst design. However, measurements are indirect and involve adsorption isotherm models, which potentially reduces the reliability of the extracted energy values. Computational, implicit solvation models predict exergonic solvation effects for phenol adsorption, failing to agree with measurements even qualitatively. In this study, an explicit, hybrid quantum mechanical/molecular mechanical approach for computing solvation free energies of adsorption is developed, solvation free energies of phenol adsorption are computed, and experimental data for solvation free energies of phenol adsorption are reanalyzed using multiple adsorption isotherm models. Explicit solvation calculations predict an endergonic solvation free energy for phenol adsorption that agrees well with measurements to within the experimental and force field uncertainties. Computed adsorption free energies of solvation of carbon monoxide, ethylene glycol, benzene, and phenol over the (111) facet of Pt and Cu suggest that liquid water destabilizes all adsorbed species, with the largest impact on the largest adsorbates.

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

The reaction mechanism of the Ideonella sakaiensis PETase enzyme

Abstract Polyethylene terephthalate (PET), the most abundantly produced polyester plastic, can be depolymerized by the Ideonella sakaiensis PETase enzyme. Based on multiple PETase crystal structures, the reaction has been proposed to proceed via a two-step serine hydrolase mechanism mediated by a serine-histidine-aspartate catalytic triad. To elucidate the multi-step PETase catalytic mechanism, we use transition path sampling and likelihood maximization to identify optimal reaction coordinates for the PETase enzyme. We predict that deacylation is likely rate-limiting, and the reaction coordinates for both steps include elements describing nucleophilic attack, ester bond cleavage, and the “moving-histidine” mechanism. We find that the flexibility of Trp185 promotes the reaction, providing an explanation for decreased activity observed in mutations that restrict Trp185 motion. Overall, this study uses unbiased computational approaches to reveal the detailed reaction mechanism necessary for further engineering of an important class of enzymes for plastics bioconversion.

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

Computational quantum chemistry of metal–organic frameworks

Metal–organic frameworks (MOFs) have premium exceptional properties for a variety of functions, such as gas separation and storage and catalysis. The large variety of possible inorganometallic nodes and organic linkers provide an almost unlimited number of combinations for assembling MOFs, which makes the experimental characterization and examination of all potentially useful combinations practically impossible. Furthermore, experimental studies of MOFs typically fall short in uncovering crucial details regarding their mechanisms of action or the molecular details responsible for their functional properties, such as the nature of adsorbate binding or the structures of transition states. Computational modeling has, therefore, become an efficient and important tool for strategizing the functionalization of MOFs and explicating the mechanisms of their functions. Furthermore, we review the computational methodologies used for computational studies of MOFs, especially Kohn–Sham density functional theory and combined quantum mechanical and molecular mechanical methods for calculating their structural, electronic, and magnetic properties, as well as for understanding the mechanisms of MOFs' applications to magetic devices, thermal conduction, gas adsorption, separation, storage, and sensing, thermal catalysis, photocatalysis, and electrocatalysis.

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

The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome

Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z ⇌ E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. In this work, we have studied a single-domain bilin-binding photoreceptor All2699g1 ( Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (P r ) and far red-absorbing (P fr ) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the P r form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ~300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Unveiling the catalytic mechanism of GTP hydrolysis in microtubules

Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice versa. Depolymerization is coupled with hydrolysis of guanosine triphosphate (GTP) within β-tubulin. Hydrolysis is favored in the MT lattice compared to a free heterodimer with an experimentally observed rate increase of 500- to 700-fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the β-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP state and whether a “compacted” GDP-state lattice is required for hydrolysis. In this work, extensive quantum mechanics/molecular mechanics simulations with transition-tempered metadynamics free-energy sampling of compacted and expanded interdimer complexes, as well as a free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice, disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to a free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip.

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

Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck–Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck–Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck–Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗