Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular activity”

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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Accelerating σ-Bond Metathesis at Sn(II) Centers

Molecular main-group hydride catalysts are attractive as cheap and Earth-abundant alternatives to transition-metal analogues. In the case of the latter, specific steric and electronic tuning of the metal center through ligand choice has enabled the iterative and rational development of superior catalysts. Analogously, building a deeper understanding of electronic structure-activity relationships for molecular main-group hydrides should facilitate the development of superior main-group hydride catalysts. Herein we report a modular Sn–Ni bimetallic system in which we systematically vary the ancillary ligand on Ni, which in turn tunes the Sn center. This tuning is probed using Sn L 1 XAS as a measure of electron density at the Sn center. We demonstrate that increased electron density at Sn centers accelerates the rate of σ-bond metathesis, and we employ this understanding to develop a highly active Sn-based catalyst for the hydroboration of CO 2 using pinacolborane. Additionally, we demonstrate that engineering London dispersion interactions within the secondary coordination sphere of Sn allows for further rate acceleration. Furthermore, these results show that the electronics of main group catalysts can be controlled without the competing effects of geometry perturbations, and that this manifests in substantial reactivity differences.

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

Catalytic oxidative coupling of arenes and alkanes: applications for efficient chemical synthesis and for hydrocarbon oligomerization. Progress Report 2016-7. Final report

This is the final report for DE-FG02-08ER15997 with a grant period of 8/15/2008-8/14/2018 (plus 1 year NCE); Program: Basic Energy Sciences; PI: Melanie S. Sanford; co-PI: Adam J. Matzger. The project resulted in 20 publications, 12 supported entirely by this grant and 8 supported substantially by this grant. The overall goals of this project were design catalysts (both homogeneous catalysts and MOF-supported catalysts) to control reactivity and selectivity in energy relevant C–H bond functionalization reactions. The proposed research led to a variety of new catalysts and catalytic processes which are currently finding application in organic synthesis. These efforts were well aligned with the goals of the DOE BES Catalysis Science Program. C–H functionalization reactions have extensive applications in energy-related industries, including petroleum and biofuels processing. The research activities also matched many of the priority areas identified by the Catalysis Science Program, including: investigating problems at the interface of heterogeneous and homogeneous catalysis as a means to derive new catalysts; incorporating 2° interactions to modulate catalyst stability, reactivity, and selectivity; using these new catalysts to tune molecular-level catalytic activity and selectivity; and studying structure-reactivity relationships of inorganic, organic, or hybrid catalytic materials in solution.

02 PETROLEUM↗
DOE OSTI2020

Mechanocatalytic Ammonia Synthesis over TiN in Transient Microenvironments

Environmentally friendly and energy-efficient ways to produce ammonia are essential to meet global food demands. In this study, a new approach for ammonia production at nominally ambient conditions is introduced. As proof of concept, ammonia is synthesized mechanocatalytically by ball milling titanium in a continuous gas flow. The ammonia synthesis reaction is proposed to follow a transient Mars–van Krevelen mechanism under mechanically activated conditions, where molecular nitrogen incorporation into the titanium lattice and titanium nitride hydrogenation occur in thermodynamically distinct environments. X-ray powder diffraction and X-ray absorption spectroscopy confirm the formation of titanium nitride from titanium and N2. The reactivity of nitrided titanium supports that lattice nitrogen plays a role in ammonia formation. The in situ formed titanium nitride is catalytically active, and the nitride regeneration reaction is determined to be the rate-limiting step. A preliminary technoeconomic analysis shows that this approach could be feasible for distributed ammonia production.

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

Deficiency in transmitter release triggers homeostatic transcriptional changes that increase presynaptic excitability

Weakening of synaptic transmission at theDrosophilalarval neuromuscular junction triggers two forms of homeostatic compensation, one that increases the probability of glutamate release per action potential (P r ) and another that increases motoneuron (MN) activity. We investigated the molecular changes in MNs that underlie the increase in MN activity. RNA sequencing (RNA-seq) analysis on MNs whose glutamate release is weakened by knockdown of components of the MN transmitter release machinery reveals a reduction in expression of a group of genes that encode potassium channels and their positive modulators. These results identify a mechanism of compensation for weakened synaptic transmission by MNs, which engages a transcriptional program in those cells to increase firing and, thereby, ensure sufficient locomotory drive.

Science & Technology - Other Topics↗
DOE OSTI2025

Dynamic molecular architecture of the synaptonemal complex

During meiosis, pairing between homologous chromosomes is stabilized by the assembly of the synaptonemal complex (SC). The SC ensures the formation of crossovers between homologous chromosomes and regulates their distribution. However, how the SC regulates crossover formation remains elusive. We isolated an unusual mutation in Caenorhabditis elegans that disrupts crossover interference but not SC assembly. This mutation alters the unique C terminal domain of an essential SC protein, SYP-4, a likely ortholog of the vertebrate SC protein SIX6OS1. We use three-dimensional stochastic optical reconstruction microscopy (3D-STORM) to interrogate the molecular architecture of the SC from wild-type and mutant C. elegans animals. Using a probabilistic mapping approach to analyze super-resolution image data, we detect changes in the organization of the synaptonemal complex in wild-type animals that coincide with crossover designation. We also found that our syp-4 mutant perturbs SC architecture. Our findings add to growing evidence that the SC is an active material whose molecular organization contributes to chromosome-wide crossover regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Ultrafast x-ray imaging of coherently controlled molecular dynamics in real space and time

Coherent control aims to manipulate chemical processes on the latent length and timescales of atoms and bonds, scales that are intrinsic to molecular dynamics but not directly resolved by most experimental probes. As a result, existing coherent-control experiments, which overwhelmingly rely on spectroscopic observables, leave a crucial blind spot: the direct, real-space recovery of all atomic and molecular rearrangements in response to coherently controlled excitations. Here, we overcome this limitation by integrating a Tannor-Kosloff-Rice pump-control-probe scheme with ultrafast X-ray scattering to capture snapshots of the wavepacket motion in a benchmark molecular system. We demonstrate this by photoexciting diatomic iodine vapor with a visible pump pulse, selectively steering the wavepacket toward ground-state recombination or dissociative pathways with a time-delayed near-IR control pulse, and recording the dynamics with angstrom and femtosecond precision with an ultrashort hard X-ray probe pulse. By comparing these structural observations with numerical solutions of the time-dependent Schrödinger equation, we reveal how coherent control actively reshapes the molecular charge density distribution. Our results pave the way for leveraging structural feedback as a control handle and provide a fundamental microscopic visualization of quantum decoherence and energy redistribution at the atomic level.

Hopper, Thomas R. [SLAC National Accelerator Labor↗
DOE OSTI2026

Molecular Design Principles for Photosystem I-Based Biohybrid Solar Fuel Catalysts

Direct solar-to-chemical conversion offers a compelling route to clean, dispatchable energy. Photosystem I (PSI), an evolutionarily optimized light-driven oxidoreductase, can be repurposed for solar-fuel production by coupling its photochemistry to catalytic interfaces. However, the molecular determinants that govern productive electron transfer to abiotic catalysts remain poorly understood. Here, we present molecular structures of active PSI-Pt nanoparticle (PtNP) biohybrids that reveal how protein architecture controls catalyst access, binding geometry, and photocatalytic efficiency. Removal of stromal subunits exposes the electron transfer chain and enables PtNP binding proximal to the F X cluster, demonstrating that steric occlusion limits access to native acceptor regions in PSI. In contrast, in trimeric PSI, PtNPs bind at multiple sites per monomer, but only a subset are positioned within electron transfer distance of terminal cofactors, resulting in a heterogeneous population of productive and nonproductive configurations. Structural analyses and molecular dynamics simulations define the interface topology, electrostatics, and cofactor-to-nanoparticle distances that govern catalyst binding and electron transfer. These results establish that catalytic inefficiency arises not only from intrinsic electron transfer constraints but also from the distribution of binding geometries imposed by the protein scaffold. Together, these findings provide a molecular framework linking protein structure to biohybrid function and define design principles for engineering PSI-based solar fuel systems and protein-nanomaterial interfaces for light-driven catalysis.

biohybrid↗
DOE OSTI2025

Binding and Translocation of Substrate Allosterically Promotes Functional Interactions Within the AlkB–AlkG Electron Transfer Complex

The alkane monooxygenase AlkB and rubredoxin AlkG form an electron transfer complex that hydroxylates terminal alkanes to produce alcohols. The recent cryoEM study of Fontimonas thermophila AlkB-AlkG complex revealed its architecture, including a dodecane (D12) substrate at the active site. However, FtAlkBG molecular mechanism of action of remains unknown. Here, in this study, we examined its dynamics and interactions by multiscale computations, including molecular dynamics simulations, elastic network models, and QM/MM of the oxygen activation mechanism at the AlkB catalytic site. D12 maintained stable interactions within the catalytic site during two MD runs, coordinated by hydrophobic residues L263-L264, I267, I133. A third extended run revealed that D12 could translocate to a membrane-exposed site near S49/F46 along a hydrophobic channel gated by I54. During this translocation, D12 was temporarily stabilized at intermediate sites IS1 (lined by I27/L30-G31/G50/L53-I54/P59/S124/A127-V128) and IS2 (I33-G34/L37/L45-F46/S49) before nearly exiting the protein, and diffused back to the active site, assisted by L30. Substrate binding and translocation across those intermediate sites affects the coupling between the iron centers in AlkBG, and interfacial interactions between AlkB-AlkG. The channel was further connected to the cytosol, near two surface-exposed arginines, potentially allowing for O 2 passage. The allosteric effects between D12 putative entry site, catalytic site and AlkB-AlkG interface were analyzed by ENM-based methods which confirmed the cooperative perturbation-responses and strongly correlated movements of residues belonging to those distal regions. Our study provides new mechanistic insights into key sites and their interactions that could be targeted for developing AlkB-variants with desirable alkane conversion functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Understanding the Origin of Highly Selective CO 2 Electroreduction to CO on Ni,N‐doped Carbon Catalysts

Abstract Ni,N‐doped carbon catalysts have shown promising catalytic performance for CO 2 electroreduction (CO 2 R) to CO; this activity has often been attributed to the presence of nitrogen‐coordinated, single Ni atom active sites. However, experimentally confirming Ni−N bonding and correlating CO 2 reduction (CO 2 R) activity to these species has remained a fundamental challenge. We synthesized polyacrylonitrile‐derived Ni,N‐doped carbon electrocatalysts (Ni‐PACN) with a range of pyrolysis temperatures and Ni loadings and correlated their electrochemical activity with extensive physiochemical characterization to rigorously address the origin of activity in these materials. We found that the CO 2 R to CO partial current density increased with increased Ni content before plateauing at 2 wt % which suggests a dispersed Ni active site. These dispersed active sites were investigated by hard and soft X‐ray spectroscopy, which revealed that pyrrolic nitrogen ligands selectively bind Ni atoms in a distorted square‐planar geometry that strongly resembles the active sites of molecular metal–porphyrin catalysts.

Koshy, David M.↗
DOE OSTI2025

Is a Malleable Active Site Loop the Key to High Substrate Promiscuity? Hybrid, Biocatalytic Route to Structurally Diverse Taxoid Side Chains with Remarkable Dual Stereocontrol

Abstract These studies reveal the first structure ofClostridium acetobutylicumalcohol dehydrogenase (CaADH), a protein exhibiting remarkable substrate promiscuity and stereochemical fidelity. The CaADH enzyme is utilized here for synthesizing 20 potential aryl isoserine side chains for the Taxotere family of tubulin‐binding chemotherapeutics. The approach involves dynamic reductive kinetic resolution (DYRKR) upon the corresponding α‐chloro‐β‐keto esters, showing high D‐synstereoselectivity, including those leading to the clinically relevant milataxel (Ar = 2‐furyl) and simotaxel (Ar = 2‐thienyl) side chains. Furthermore, various cross‐coupling chemistries performed on thep‐bromophenyl isoserine side chain significantly enhance the structural diversity of the taxoid side chain library obtained (16 additional taxoid side chains). The CaADH structure is notable: (i) the nicotinamide cofactor is bound in ananti‐conformation, with the amide carbonyl occupying the ketone binding pocket, and (ii) a flexible loop near the active site likely contributes to the remarkable substrate promiscuity observed in CaADH. We present our perspective on the dynamic nature of the CaADH active site through molecular dynamics simulation, proposing a halogen bonding model as a potential mechanism for the remarkable selectivity for an (S)‐configured C─Cl bond, in addition to the D‐facial selectivity, demonstrated across 20 diverse substrates by this remarkable short‐chain dehydrogenase enzyme.

Chemistry↗
DOE OSTI2021

First-Principles Study of Interaction between Molecules and Lewis Acid Zeolites Manipulated by Injection of Energized Charge Carriers

Metal dopants in Lewis acid zeolites can be applied to manipulate the interaction between the active sites and molecular reactants. However, only a few elements can be introduced into the zeolite framework to generate strong Lewis acid sites. In this study, we propose an alternative approach to tune the interaction between zeolite and molecules by introducing energized charge carriers that are photoexcited in a complex of plasmonic metal and zeolites. Here, through density functional theory (DFT) calculations, we show that although the energized electrons do not impact the adsorption of ammonia, which is used as a probe molecule, on Zr- and Si-BEA, ammonia’s heat of adsorption can be reduced up to 60% on Sn-BEA and 20% on Ti-BEA, respectively, because of the localized population of the electrons at the Sn and Ti center. This most pronounced effect in Sn-BEA is attributed to the Sn-induced midgap states and the strong electronegativity of Sn atoms. In contrast, the energized holes can strengthen the interaction between zeolites and ammonia by at least 10%. Particularly, if an energized hole is present in the system, the heat of adsorption of ammonia within Si-BEA can increase 3-fold, shifting from weak to moderate interaction. We find that, similar to closed sites, the effect of energized charge carriers can also be extended to open sites of Lewis acid zeolites. Our study provides fundamental insights for unlocking the potentials of integrating plasmonic metals with zeolites and brings an additional degree of control to tune the interfacial interaction.

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

Maximized Hole Trapping in a Polystyrene Transistor Dielectric from a Highly Branched Iminobis(aminoarene) Side Chain

We synthesized highly branched and electron donating side chain subunits and attached them to polystyrene (PS) used as a dielectric layer in a pentacene field effect transistor. The influence of these groups on dielectric function, charge retention and threshold voltage shifts (ΔV th ) depending on their positions in dielectric multilayers was determined. We compared the observations made on an N-perphenylated iminobisaniline side chain with those from the same side chains modified with ZnO nanoparticles and with an adduct formed from tetracyanoethylene (TCNE). We also synthesized an analogue in which six methoxy groups are present instead of two amine nitrogens. At 6 mol % side chain, hopping transport was sufficient to cause shorting of the gate, while at 2 mol %, charge trapping was observable as transistor threshold voltage shifts (ΔV th ). Here, we created three types of devices: with the substituted PS layer as single layer dielectric, on top of a crosslinked PS layer but in contact with the pentacene (bilayers), and sandwiched between two PS layers in trilayers. Particularly large bias stress effects and ΔV th , larger than the hexamethoxy and previously studied dimethoxy analogs, were observed in the second case and the effects increased with the increasing electron donating properties of the modified side chains. The highest ΔV th was consistent with a majority of the side chains stabilizing trapped charge. Trilayer devices showed decreased charge storage capability compared to previous work in which we used less donating side chains but in higher concentrations. The ZnO and TCNE modifications resulted in slightly more and less negative ΔV th , respectively, when the side chain polystyrene was not in contact with the pentacene and isolated from the gate electrode. The results indicate a likely maximum combination of molecular charge stabilizing activity and side chain concentration that still allows gate dielectric function.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex

The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Can ferric-oxyl excited states explain elongated iron-oxygen bonds in heme peroxidase catalytic intermediates?

The use of X-ray structures to determine and interpret the ferryl iron-oxygen bond order in molecular oxygen-activating heme enzymes has, in the past, been controversial. This has mainly stemmed from the susceptibility of ferryl species to X-ray-induced electronic state changes. In this work we establishe using time-resolved serial femtosecond X-ray crystallography (tr-SFX) on a dye-decolourising peroxidase that the ferryl intermediate species (Compounds I and II) captured following in situ mixing of microcrystals with H 2 O 2 have single, rather than the double bond character expected. X-ray emission validated tr-SFX data with quantum refinement, time-dependent-DFT calculations and QM/MM geometry optimizations together support the concept that the single iron-oxygen bond character is not an indication of ferryl reduction or a protonated form (Fe IV -OH) but is instead attributed to the existence of accessible excited states possessing ferric-oxyl (Fe III –O •– ) character. Such states offer insight into the nature of ferryl heme.

Williams, Lewis J. [University of Essex, Colcheste↗
DOE OSTI2025

Transforming an ATP-dependent enzyme into a dissipative, self-assembling system

Nucleoside triphosphate (NTP)-dependent protein assemblies such as microtubules and actin filaments have inspired the development of diverse chemically fueled molecular machines and active materials but their functional sophistication has yet to be matched by design. Given this challenge, we asked whether it is possible to transform a natural adenosine 5'-triphosphate (ATP)-dependent enzyme into a dissipative self-assembling system, thereby altering the structural and functional mode in which chemical energy is used. Furthermore we report that FtsH (filamentous temperature-sensitive protease H), a hexameric ATPase involved in membrane protein degradation, can be readily engineered to form one-dimensional helical nanotubes. FtsH nanotubes require constant energy input to maintain their integrity and degrade over time with the concomitant hydrolysis of ATP, analogous to natural NTP-dependent cytoskeletal assemblies. Yet, in contrast to natural dissipative systems, ATP hydrolysis is catalyzed by free FtsH protomers and FtsH nanotubes serve to conserve ATP, leading to transient assemblies whose lifetimes can be tuned from days to minutes through the inclusion of external ATPases in solution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (M pro also known as 3CL pro ) is a primary drug target, due to its essential role in maturation of the viral polyproteins. In this study, we provide crystallographic evidence, along with some binding assay data, that three clinically approved anti hepatitis C virus drugs and two other drug-like compounds covalently bind to the M pro Cys145 catalytic residue in the active site. Also, molecular docking studies can provide additional insight for the design of new antiviral inhibitors for SARS-CoV-2 using these drugs as lead compounds. One might consider derivatives of these lead compounds with higher affinity to the M pro as potential COVID-19 therapeutics for further testing and possibly clinical trials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Filming enhanced ionization in an ultrafast triatomic slingshot

Abstract Filming atomic motion within molecules is an active pursuit of molecular physics and quantum chemistry. A promising method is laser-induced Coulomb Explosion Imaging (CEI) where a laser pulse rapidly ionizes many electrons from a molecule, causing the remaining ions to undergo Coulomb repulsion. The ion momenta are used to reconstruct the molecular geometry which is tracked over time (i.e., filmed) by ionizing at an adjustable delay with respect to the start of interatomic motion. Results are distorted, however, by ultrafast motion during the ionizing pulse. We studied this effect in water and filmed the rapid “slingshot” motion that enhances ionization and distorts CEI results. Our investigation uncovered both the geometry and mechanism of the enhancement which may inform CEI experiments in many other polyatomic molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗