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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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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Effect of Mutation and Substrate Binding on the Stability of Cytochrome P450 BM3 Variants

Cytochrome P450 BM3 is a heme-containing enzyme from Bacillus megaterium that displays high monooxygenase activity and has a self-sufficient electron transfer system in the full-length enzyme. Its potential synthetic applications drive protein engineering efforts to produce variants capable of oxidizing nonnative substrates such as pharmaceuticals and aromatic pollutants. However, promiscuous P450 BM3 mutants often exhibit lower stability, thereby hindering their industrial application. This study demonstrated that the heme domain R47L/F87V/L188Q/E267V/F81I pentuple mutant (PM) is destabilized because of the disruption of hydrophobic contacts and salt bridge interactions. This was directly observed from crystal structures of PM in the presence and absence of ligands (palmitic acid and metyrapone). The instability of the tertiary structure and heme environment of substrate-free PM was confirmed by pulse proteolysis and circular dichroism, respectively. Binding of the inhibitor, metyrapone, significantly stabilized PM, but the presence of the native substrate, palmitic acid, had no effect. On the basis of high-temperature molecular dynamics simulations, the lid domain, β-sheet 1, and Cys ligand loop (a β-bulge segment connected to the heme) are the most labile regions and, thus, potential sites for stabilizing mutations. Possible approaches to stabilization include improvement of hydrophobic packing interactions in the lid domain and introduction of new salt bridges into β-sheet 1 and the heme region. An understanding of the molecular factors behind the loss of stability of P450 BM3 variants therefore expedites site-directed mutagenesis studies aimed at developing thermostability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin

Thrombin exists as an ensemble of active (E) and inactive (E*) conformations that differ in their accessibility to the active site. Here we show that redistribution of the E*–E equilibrium can be achieved by perturbing the electrostatic properties of the enzyme. Removal of the negative charge of the catalytic Asp102 or Asp189 in the primary specificity site destabilizes the E form and causes a shift in the 215–217 segment that compromises substrate entrance. Solution studies and existing structures of D102N document stabilization of the E* form. A new high-resolution structure of D189A also reveals the mutant in the collapsed E* form. Furthermore, these findings establish a new paradigm for the control of the E*–E equilibrium in the trypsin fold.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

A Molecular Mechanism for Nonphotochemical Quenching in Cyanobacteria

The cyanobacterial orange carotenoid protein (OCP) protects photosynthetic cyanobacteria from photodamage by dissipating excess excitation energy collected by phycobilisomes (PBS) as heat. Dissociation of the PBS–OCP complex in vivo is facilitated by another protein known as the fluorescence recovery protein (FRP), which primarily exists as a dimeric complex. In this work, we used various mass spectrometry (MS)-based techniques to investigate the molecular mechanism of this FRP-mediated process. FRP in the dimeric state (dFRP) retains its high affinity for the C-terminal domain (CTD) of OCP in the red state (OCP r ). Site-directed mutagenesis and native MS suggest the head region on FRP is a candidate to bind OCP. After attachment to the CTD, the conformational changes of dFRP allow it to bridge the two domains, facilitating the reversion of OCPr into the orange state (OCP o ) accompanied by a structural rearrangement of dFRP. Interestingly, we found a mutual response between FRP and OCP; that is, FRP and OCP r destabilize each other, whereas FRP and OCP o stabilize each other. A detailed mechanism of FRP function is proposed on the basis of the experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies

Human liver glycerol 3-phosphate dehydrogenase (hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme–substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E·NAD, and ternary E·NAD·DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. Here, these results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Crystal Structure of d -Ornithine/ d -Lysine Decarboxylase, a Stereoinverting Decarboxylase: Implications for Substrate Specificity and Stereospecificity of Fold III Decarboxylases

A newly discovered Fold III pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, d-ornithine/lysine decarboxylase (DOKDC), catalyzes decarboxylation of d-lysine and d-ornithine with inversion of stereochemistry. The X-ray crystal structure of DOKDC has been determined to 1.72 Å. DOKDC has a low level of sequence identity (<30%) with meso-diaminopimelate decarboxylase (DAPDC) and l-lysine/ornithine decarboxylase (LODC), but its three-dimensional structure is very similar. The distal binding site of DAPDC contains a conserved arginine that forms an ion pair with the l-carboxylate end of DAP. In both LODC and DOKDC, this distal site is modified by replacement of the arginine with aspartate, changing the substrate specificity. l-Ornithine decarboxylase (ODC) and LODC have a conserved phenylalanine on the re-face of the PLP complex that has been found to play a key role in the decarboxylation mechanism. We have found that both DAPDC and DOKDC have tyrosine instead of phenylalanine at this position, which precludes the binding of l-amino acids. Because the PLP-binding lysine in ODC, LODC, DAPDC, and DOKDC is located on the re-face of the PLP, we propose that this is the acid group responsible for protonation of the product, thus resulting in the observed retention of configuration for decarboxylation of l-amino acids and inversion for decarboxylation of d-amino acids. Here, the reactions of DAPDC and DOKDC are likely accelerated by positive electrostatics on the re-face by the lysine ε-ammonium ion and on the si-face by closure of the lid over the active site, resulting in desolvation and destabilization of the d-amino acid carboxylate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Inhibition of Microtubule Depolymerization by Osmolytes

Microtubule dynamics play a critical role in the normal physiology of eukaryotic cells as well as a number of cancers and neurodegenerative disorders. The polymerization/depolymerization of microtubules is regulated by a variety of stabilizing and destabilizing factors, including microtubule-associated proteins and therapeutic agents (e.g., paclitaxel, nocodazole). Here in this paper, we describe the ability of the osmolytes polyethylene glycol (PEG) and trimethylamine-N-oxide (TMAO) to inhibit the depolymerization of individual microtubule filaments for extended periods of time (up to 30 days). We further show that PEG stabilizes microtubules against both temperature- and calcium-induced depolymerization. Our results collectively suggest that the observed inhibition may be related to combination of the kosmotropic behavior and excluded volume/osmotic pressure effects associated with PEG and TMAO. Lastly, taken together with prior studies, our data suggest that the physiochemical properties of the local environment can regulate microtubule depolymerization and may potentially play an important role in in vivo microtubule dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Direct Determination of Hydroxymethyl Conformations of Plant Cell Wall Cellulose Using 1 H Polarization Transfer Solid-State NMR

In contrast to the well-studied crystalline cellulose of microbial and animal origins, cellulose in plant cell walls is disordered due to its interactions with matrix polysaccharides. Plant cell wall (PCW) is an undisputed source of sustainable global energy; therefore, it is important to determine the molecular structure of PCW cellulose. The most reactive component of cellulose is the exocyclic hydroxymethyl group: when it adopts the tg conformation, it stabilizes intrachain and interchain hydrogen bonding, while gt and gg conformations destabilize the hydrogen-bonding network. So far, information about the hydroxymethyl conformation in cellulose has been exclusively obtained from 13 C chemical shifts of monosaccharides and oligosaccharides, which do not reflect the environment of cellulose in plant cell walls. Here, we use solid-state Nuclear Magnetic Resonance (ssNMR) spectroscopy to measure the hydroxymethyl torsion angle of cellulose in two model plants, by detecting distance-dependent polarization transfer between H4 and H6 protons in 2D 13 C– 13 C correlation spectra. We show that the interior crystalline portion of cellulose microfibrils in Brachypodium and Arabidopsis cell walls exhibits H4–H6 polarization transfer curves that are indicative of a tg conformation, whereas surface cellulose chains exhibit slower H4–H6 polarization transfer that is best fit to the gt conformation. Joint constraints by the H4–H6 polarization transfer curves and 13 C chemical shifts indicate that it is unlikely for interior cellulose to have a significant population of the gt and gg conformation mixed with the tg conformation, while surface cellulose may adopt a small percentage of the gg conformation. These results provide new constraints to the structure and matrix interactions of cellulose in plant cell walls, and represent the first direct determination of a torsion angle in an important noncrystalline carbohydrate polymer.

09 BIOMASS FUELS↗
DOE OSTI2015

Capable Cross-links: Polymersomes Reinforced with Catalytically Active Metal–Ligand Bonds

Polymersomes, hollow spherical nano-to-microscale polymer assemblies, have increasingly become important constructs in the development of biomimetic materials that expand the library of functional and robust analogs to lipid-based vesicles. As compared to liposomes, polymersomes possess superior physical properties and the nearly unlimited potential for synthetic fine-tuning. Here in this paper, we improve on the physical properties of these polymer vesicles by introducing platinum-based metal–ligand cross-links into the hydrophobic core, which gave the vesicles demonstrated resistance to destabilization by surfactants over un-cross-linked polymersomes. The formation of cross-links was capable of being selectively reversed by the addition of phosphines. In addition, the Pt(0) cross-links retained their catalytic activity for the hydrosilylation of alkenes.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Design Principles in Engineering of Multigrain Nanocatalysts via Multiscale Electronic Structure Characterization

Engineering grain boundary (GB) strain provides a promising pathway to tune the catalytic properties of nanocrystals. However, structural heterogeneity from random grain orientation and geometry has limited clear structure–property correlations. Here, we utilize a multigrain Co3O4/Mn3O4 core/shell nanocrystal platform as a model system to systematically investigate how geometric misfit strain at GBs serves as catalytically active sites for the oxygen reduction reaction. Through precise subnanometer-level control over grain morphology and by integrating multiscale electronic structure characterization, we identify the electronic structural signature of GB defects and establish a direct correlation between localized strain fields and modified electronic states. Strain modulation at GBs alters the eg orbital energy levels, with elongation along the z-axis combined with shear strain stabilizing the eg states, in contrast to the destabilization observed under pure shear strain. This stabilization mechanism enhances the electrocatalytic activity and selectivity of strained GBs compared with strain-relaxed grain surfaces. Furthermore, we reveal that GBs exhibit a radial strain gradient, producing a spatial energy shift that further modulates local electronic structures, as resolved through the classification of electron energy loss spectroscopy data. Together, these findings demonstrate that geometric misfit strain enables precise tuning of grain geometry and the resulting electronic structures, offering a robust strategy for engineering next-generation nanocatalysts.

Cho, Min Gee↗
DOE OSTI2025

Annealing-Driven Phase Control Enables Plasmonic Tunability in Alloy Nanoparticles

A critical aspect of designing and realizing useful solid state materials is controlling phase and structure to tailor physical properties. While common for semiconductor and quantum materials, plasmonic materials have inhabited a narrow phase space typically comprising one or two elements, e.g., face-centered cubic metals. While this simplicity has enabled robust use and understanding of Au and Ag nanoparticles, it has also limited the design and manipulation of solid state properties. Here, we show that by tuning the phase and elemental composition of binary Au−Sn nanoparticles, the steady-state absorbance and ultrafast thermalization properties of plasmonic nanoparticles can be controlled. Solid state characterization suggests this is due to the dealloying of Sn and destabilization of the AuSn phase, leading to higher quality Au 5 Sn intermetallic phases alongside Au. Consequently, this work shows that phase control can profoundly influence the properties of plasmonic nanoparticles, providing important tunability for applications in catalysis, photothermal heating, and sensing.

Gold↗
DOE OSTI2017

Cs 1– x Rb x PbCl 3 and Cs 1– x Rb x PbBr 3 Solid Solutions: Understanding Octahedral Tilting in Lead Halide Perovskites

The structures of the lead halide perovskites CsPbCl3 and CsPbBr3 have been determined from X-ray powder diffraction data to be orthorhombic with Pnma space group symmetry. Their structures are distorted from the cubic structure of their hybrid analogs, CH3NH3PbX3 (X = Cl, Br), by tilts of the octahedra (Glazer tilt system a–b+a–). Substitution of the smaller Rb+ for Cs+ increases the octahedral tilting distortion and eventually destabilizes the perovskite structure altogether. To understand this behavior, bond valence parameters appropriate for use in chloride and bromide perovskites have been determined for Cs+, Rb+, and Pb2+. As the tolerance factor decreases, the band gap increases, by 0.15 eV in Cs1–xRbxPbCl3 and 0.20 eV in Cs1–xRbxPbBr3, upon going from x = 0 to x = 0.6. The band gap shows a linear dependence on tolerance factor, particularly for the Cs1–xRbxPbBr3 system. Comparison with the cubic perovskites CH3NH3PbCl3 and CH3NH3PbBr3 shows that the band gaps of the methylammonium perovskites are anomalously large for APbX3 perovskites with a cubic structure. This comparison suggests that the local symmetry of CH3NH3PbCl3 and CH3NH3PbBr3 deviate significantly from the cubic symmetry of the average structure.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Bridging Transition Metal and Anion Redox Processes in Li-Rich Sulfide Cathodes

Li-ion batteries are essential for decarbonizing global transport and energy, but their scalability is constrained by limited supplies of critical cathode elements, such as Ni, Mn, Co, and P. To address this, we previously introduced high-energydensity Li-ion cathodes composed of Al, Fe, and S, which are elements already produced globally at industrial scale and batterygrade purity. These cathodes leverage sulfide anion redox, involving nonbonding S 3p states and localized distortions that form and break S−S bonds, enabling high capacity. Here, we expand this chemical space by incorporating Cu into cathodes Li 2.2d−z Cu z Al 0.2 Fe 0.6 S 2 (0 ≤ z ≤ 0.4), where highly covalent Cu−S interactions stabilize holes on Cu as Cu >1+ . This Cu redox extends charge compensation that was previously restricted to localized, electronically isolated S−S bonds. Cu also limits capacity, which we attribute to structural destabilization of the delithiated phase, despite the thermodynamic stability of Cu >1+ . By describing the effects of Cu on charge compensation and phase stability, we present a sulfide anion redox mechanism for next-generation multielectron redox Li-ion cathodes, where highly covalent transition metal states participate in otherwise electronically isolated redox processes involving anion nonbonding states.

Anions↗
DOE OSTI2020

Reformulated Red mud: a robust catalyst for in situ catalytic pyrolysis of biomass

Biomass feedstocks contain inorganic compounds generally classified as ash. The ash consists of compounds of potassium, calcium, magnesium, silicon, phosphorous and other elements. These elements have been reported to influence both the pyrolysis reactions as well as destabilizing the pyrolysis oils during storage. The inorganic elements have also been reported to deposit on catalyst surfaces during in situ catalytic pyrolysis leading to the eventual deactivation of acidic catalysts such as zeolites. The deposition of inorganic elements and their effect on formulated red mud (FRM) catalyst during in situ catalytic pyrolysis of pinyon juniper wood was investigated. The inorganic elements were measured for the fresh, coked, and regenerated catalysts. The BET specific surface area of the FRM catalyst decreased from 76 m2/g for the fresh catalyst to 53 m2/g for the stable regenerated catalyst. After three regenerations, the BET specific surface area stabilized at 53 m2/g and remained constant after all other regenerations. Potassium, calcium, magnesium, and phosphorous were deposited on the catalyst. Potassium deposition was linear with the number of regenerations while magnesium and calcium depositions were initially rapid but leveled off after three regenerations of the catalyst. Phosphorous deposition was almost linear, but the data were more scattered compared to potassium. The potassium deposition was attributed to physical phenomenon whereas calcium and magnesium depositions were more akin to chemical reactions related to the loss of BET surface area of the catalyst. The deposition of these elements on the surface of the catalyst did not deactivate it. After each catalyst regeneration, the oil yield was not significantly affected and the oil oxygen content and viscosity decreased slightly. This clearly showed that formulated red mud is a robust catalyst suitable for in situ catalytic fast pyrolysis of biomass.

Agblevor, Foster↗
DOE OSTI2023

ortho -Fluoro or ortho Effect? Oxidative Addition of Zerovalent Nickel into the C–CN Bond of Substituted Benzonitriles

Substitution effects on the oxidative addition of [Ni(dmpe)] to the C—CN bond of CF 3 and CH 3 substituted benzonitriles was studied by DFT and compared to their F analogs. C—CN oxidative addition products were stabilized slightly more by the first o-CF 3 group (-7.4 kcal/mol) compared to F groups (-6.6 kcal/mol per o-F), but due to steric crowding the second o-CF 3 group did not show considerably more stabilization (-0.8 kcal/mol). CH 3 groups led to destabilization.

02 PETROLEUM↗
DOE OSTI2025

Breaking the Neptunyl Barrier: Direct Access to Neptunium(IV) in Aqueous Solution via Polyoxometalate-Mediated Reduction and Stabilization

Neptunium exhibits truly unique chemistry as its speciation is dominated by the neptunyl(V) ion (NpO 2 + ). Here, in this study, we describe the spontaneous destabilization and reduction of neptunyl(V) via complexation to the Keggin-type polyoxometalate (POM) ligand PW 11 O 39 7– . The POM-mediated reduction of NpO 2 + does not require any reducing agent and occurs within minutes, at room temperature, and in aqueous solution. The resulting [Np(PW 11 O 39 ) 2 ] 10- complex (Np(PW 11 ) 2 ) remains soluble, water-stable, and air-stable for weeks and persists over an extended acidity range. Single-crystal structure, solid-state Raman and UV–visible absorbance characterization of Np(PW 11 ) 2 revealed a mixed alpha/beta isomery of the Keggin ion, forming an unprecedented 50:50 mixture of Np(α-PW 11 ) 2 and Np(α-PW 11 )(β-PW 11 ). Experiments with other tetravalent ions (i.e., Zr 4+ , Hf 4+ , Ce 4+ , and Th 4+ ) indicate that the occurrence of the beta isomer is specific to Np 4+ and independent of the cation’s size. Solution-state characterization of the Np-PW 11 system via UV-visible-NIR absorbance, 31 P NMR, VT NMR, and relaxometry further elucidated the speciation. Moreover, comparative experiments with uranium revealed that the two types of actinyl ions (UO 2 2+ vs NpO 2 + ) undergo drastically different reactions in the presence of PW 11 . UO 2 2+ is not reduced but instead uses PW 11 as a phosphate reservoir and precipitates as uranyl phosphate.

Hastings, Ashley M. [Lawrence Livermore National L↗
DOE OSTI2025

Trans-Influence in Dinuclear Pt(III) Complexes: Electronic Structure, σ-Donation, and Pt–Pt Spin–Spin Coupling

This study investigates the trans influence in dinuclear platinum(III) complexes using a combined approach of ab initio molecular dynamics and natural localized molecular orbital (NLMO) analysis. Focusing on pivalamidate-bridged Pt III complexes with axial ligands of varying σ-donation strength, it is quantified how ligand−metal interactions propagate through the Pt−Pt bond, and how they affect bond polarization, axial water coordination, and 1 J PtPt spin−spin coupling constants. NLMO analysis reveals quantitatively that strong σ-donating ligands polarize the Pt−Pt bond, shifting the electron density toward the opposite platinum center. The polarization mechanism is identified as the primary reason for the observed reduction of 1 J PtPt , because the bond polarization diminishes the transmission of the nuclear magnetic spin-induced electron spin density through the Pt−Pt bond. Additionally, the destabilization of axial water coordination at the opposite Pt site can be rationalized through a polarizationinduced Pt IV − Pt II -like mixed-valence character.

Ab initio molecular dynamics↗
DOE OSTI2022

Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase

Remdesivir was the first antiviral drug that received emergency use authorization from the United States Food and Drug Administration and is now formally approved to treat COVID-19. Remdesivir is a nucleotide analogue that targets the RNA-dependent RNA polymerase (RdRp) of coronaviruses, including SARS-CoV-2. The solution of multiple RdRp structures has been one of the main axes of research in the race against the SARS-CoV-2 virus. Several hypotheses of the mechanism of inhibition of RdRp by remdesivir have been proposed, although open questions remain. This work uses molecular dynamics simulations to explore the impact of remdesivir and two analogues as incoming nucleotides and of up to four incorporations of remdesivir along the primer strand on RdRp. The simulation results suggest that the overall structure and the dynamical behavior of RdRp are destabilized by remdesivir and the two analogues in the incoming position. The incorporation of remdesivir along the primer strand impacts specific non-bonded interactions between the nascent RNA and the polymerase subunit, as well as the overall dynamical networks on RdRp. The strongest impact on the structure and dynamics are observed after three incorporations, when remdesivir is located at position -A3, in agreement with previously reported experimental and computational results. Our results provide atomic-level details of the role played by remdesivir on the disruption of RNA synthesis by RdRp and the main drivers of these disruptions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗