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DOE OSTI2020

Mechanisms of Degradation of Toxic Nerve Agents: Quantum-chemical Insight into Interactions of Sarin and Soman with Molybdenum Dioxide

With the urgent need to provide an efficient and reliable protection for people from fatal chemical and biological weapons, our fundamental understanding of how toxins interact with filters is far from complete. The situation is further complicated by natural difficulties of performing experimental measurements with lethal toxins. Unlike experiments, computational modeling offers an attractive and safe yet reliable way of studying behavior of toxic agents on a variety of substrates at a great level of detail. Here, we report DFT-based quantum-chemical calculations of adsorption and decomposition of DMMP, sarin and soman on MoO 2 (011) surface. Our calculations show that MoO 2 strongly adsorbs toxic nerve agents and quickly decomposes them. Decomposition of DMMP on the MoO 2 (011) surface proceeds via the PO-CH 3 bond breaking and a formation of a surface methoxy group. The calculated activation barrier for this reaction is 131.5 kJ mol -1 . Unlike DMMP, decomposition of sarin and soman proceeds via the dealkylation reaction yielding propene and 3,3-dimethyl-1-butene, respectively. Decomposition of sarin requires a remarkably low energy (53.7 kJ mol- 1 ), whereas the similar reaction in soman requires 50 kJ mol -1 more energy. We also make specific predictions to guide Ambient-Pressure X-ray Photoelectron Spectroscopy (APXPS) experiments on sarin interaction with MoO 2 samples. We conclude that MoO 2 serves as an efficient substrate able of degrading toxins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Electrochemistry at a single nanoparticle: from bipolar regime to tunnelling

This work is concerned with long-distance interactions between an unbiased metal nanoparticle (NP) and a nanoelectrode employed as a tip in the scanning electrochemical microscope (SECM). A NP immobilized on the inert substrate acts as a bipolar electrode, producing positive SECM feedback. The tip current magnitude depends strongly on the ratio of the particle and tip radii and the heterogeneous charge-transfer kinetics. The onset of electron tunneling was observed at very short separation distances (<2–3 nm) at which the NP behaves as a part of the tip electrode. The rate constant of the electron-transfer (ET) or electrocatalytic reaction at the NP can be extracted from either feedback or tunneling current. The tunneling mode of SECM can be used to investigate heterogeneous reactions occurring at a single NP without making an ohmic contact with it. This technique can also help elucidate nanoparticle/electrode interactions in various electrochemical systems ranging from NPs immobilized on the electrode surface to nanoimpact collision events.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

First-Principles Calculations of van der Waals and Spin Orbit Effects on the Two-Dimensional Topological Insulator Stanene and Stanene on Ge(111) Substrate

The structural and electronic properties of the monolayer and bilayer stanene structures have been studied using first-principles calculations. For the monolayer, the buckled structure is more stable than the flat one, with an opening of the band gap when spin-orbit coupling is taken into account, as mentioned in recent studies. For the bilayer, three types of stacking are considered: parallel layers, anti-parallel layers, and parallel layers where the first layer is shifted from the second one. These three configurations are named AA1, AA2, and AB, respectively. The two layers are separated by the distance d. The interactions between two layers of stanene are strong for a short distance, while the van der Waals bonding appears for a longer distance. Furthermore, stanene was fabricated experimentally on a substrate; thus, we proposed another study of electronic properties of stanene deposited on Ge(111) to reveal other behavior as a topological insulator and show the existence of the quantum spin Hall effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Atomistic simulations for investigation of substrate effects on lipid in-source fragmentation in secondary ion mass spectrometry

In beam-based ionization methods, the substrate plays an important role on the desorption mechanism of molecules from surfaces. Both the specific orientation that a molecule adopts at a surface and the strength of the molecule-surface interaction can greatly influence desorption processes, which in turn will affect the ion yield and the degree of in-source fragmentation of a molecule. In the beam-based method of secondary ion mass spectrometry (SIMS), in-source fragmentation can be significant and molecule specific due to the hard ionization method of using a primary ion beam for molecule desorption. To investigate the role of the substrate on orientation and in-source fragmentation, we have used atomistic simulations—molecular dynamics in combination with density functional theory calculations—to explore the desorption of a sphingolipid (palmitoylsphingomyelin) from a model surface (gold). We then compare SIMS data from this model system to our modeling findings. Using this approach, we found that the combined adsorption and binding energy of certain bonds associated with the headgroup fragments (C3H8N+, C5H12N+, C5H14NO+, and C5H15PNO4+) was a good predictor for fragment intensities (as indicated by relative ion yields). This is the first example where atomistic simulations have been applied in beam-based ionization of lipids, and it presents a new approach to study biointerfacial lipid ordering effects on SIMS imaging.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Thin Film Solid State Active Dosimetry

With the many advances in semiconductor manufacturing, the pool of available materials for use in their production also continues to broaden. One such example is aluminum antimonide (AlSb). Its promising properties for radiation detection have attracted multiple researchers, and allow for the possibility that it may be a high resolution, room temperature x-ray/gamma detector. Antimony has an atomic number of 51 (Z=51) and is responsible for the majority of photon interactions. Furthermore, the mass attenuation coefficient is comparable with other well-known solid state gamma detectors such as CZT. With a band gap of 1.6 eV (CZT=1.5 eV), low leakage current at room temperature is expected, and high charge carrier statistics from radiation interactions can be expected. Charge carrier statistics are driven by high charge mobility (μ) and lifetime (τ). μτ for CZT is on the order of 5x10{sup -3} cm{sup 2}/V for electrons, but two orders of magnitude smaller for holes. This results in large variations in detector pulse height depending on the location of interaction (close to the anode vs. close to the cathode). Theoretically, AlSb should exhibit much more symmetric electron and hole properties near 5x10{sup -3} cm{sup 2}/V. According to the Hecht relation, this should produce a more uniform detector response and increase the number of generated charge carriers, improving resolution. An added benefit is that AlSb can be grown directly onto Si substrates, enabling fully integrated circuit board-level sensors. However, several characteristic properties remain unknown and inconsistent published results due to difficulties in producing the material. Difficulties in bulk growth methods (material interactions with growth hardware such as crystals and air) resulted in high levels of defects. The use of AlSb in optoelectronics from thin film growth methods has been documented, including growth directly onto Si, and provides the potential for much more controlled material. In our work we use thin film growth of AlSb geared towards high quality material for understanding the properties for radiation detection. (authors)

36 MATERIALS SCIENCE↗

DOE OSTI2019

Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction

The alarmone (p)ppGpp regulates diverse targets, yet its target specificity and evolution remain poorly understood. Here, we elucidate the mechanism by which basal (p)ppGpp inhibits the purine salvage enzyme HPRT by sharing a conserved motif with its substrate PRPP. Intriguingly, HPRT regulation by (p)ppGpp varies across organisms and correlates with HPRT oligomeric forms. (p)ppGpp-sensitive HPRT exists as a PRPP-bound dimer or an apo- and (p)ppGpp-bound tetramer, where a dimer-dimer interface triggers allosteric structural rearrangements to enhance (p)ppGpp inhibition. Loss of this oligomeric interface results in weakened (p)ppGpp regulation. Our results reveal an evolutionary principle whereby protein oligomerization allows evolutionary change to accumulate away from a conserved binding pocket to allosterically alter specificity of ligand interaction. This principle also explains how another (p)ppGpp target GMK is variably regulated across species. Since most ligands bind near protein interfaces, we propose that this principle extends to many other protein–ligand interactions.

Life Sciences & Biomedicine - Other Topics↗

DOE OSTI2019

Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Transporter annotations are holding up progress in metabolic modeling

Mechanistic, constraint-based models of microbial isolates or communities are a staple in the metabolic analysis toolbox, but predictions about microbe-microbe and microbe-environment interactions are only as good as the accuracy of transporter annotations. A number of hurdles stand in the way of comprehensive functional assignments for membrane transporters. These include general or non-specific substrate assignments, ambiguity in the localization, directionality and reversibility of a transporter, and the many-to-many mapping of substrates, transporters and genes. In this perspective, we summarize progress in both experimental and computational approaches used to determine the function of transporters and consider paths forward that integrate both. Investment in accurate, high-throughput functional characterization is needed to train the next-generation of predictive tools toward genome-scale metabolic network reconstructions that better predict phenotypes and interactions. More reliable predictions in this domain will benefit fields ranging from personalized medicine to metabolic engineering to microbial ecology.

Casey, John↗

DOE OSTI2021

Structural basis for the specificity of PPM1H phosphatase for Rab GTPases

LRRK2 serine/threonine kinase is associated with inherited Parkinson’s disease. LRRK2 phosphorylates a subset of Rab GTPases within their switch 2 motif to control their interactions with effectors. Recent work has shown that the metal-dependent protein phosphatase PPM1H counteracts LRRK2 by dephosphorylating Rabs. PPM1H is highly selective for LRRK2 phosphorylated Rabs, and closely related PPM1J exhibits no activity towards substrates such as Rab8a phosphorylated at Thr72 (pThr72). Here, we have identified the molecular determinant of PPM1H specificity for Rabs. The crystal structure of PPM1H reveals a structurally conserved phosphatase fold that strikingly has evolved a 110-residue flap domain adjacent to the active site. The flap domain distantly resembles tudor domains that interact with histones in the context of epigenetics. Cellular assays, crosslinking and 3-D modelling suggest that the flap domain encodes the docking motif for phosphorylated Rabs. Consistent with this hypothesis, a PPM1J chimaera with the PPM1H flap domain dephosphorylates pThr72 of Rab8a both in vitro and in cellular assays. Therefore, PPM1H has acquired a Rab-specific interaction domain within a conserved phosphatase fold.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Long-Chain Polysulfide Retention at the Cathode of Li–S Batteries

Lithium–sulfur batteries present a complex interconnected chemistry where the three components—anode, electrolyte, and cathode—strongly interact with each other. One of the main issues associated with these interactions is the dissolution in the electrolyte solution of part of the sulfur reduction products (mainly long-chain polysulfides) during the discharge reactions at the cathode. These dissolved species can migrate and react at the anode surface producing undesired insulating films. A potential solution to mitigate this problem is to resort to additional materials which can act as anchors of the soluble species thus avoiding their migration. Density functional theory and ab initio molecular dynamics simulations are employed to investigate the ability of certain substrates to retain long-chain polysulfides (Li 2 S 6 and Li 2 S 8 ) at their surfaces in the presence of a pure solvent or a lithiated solution. Nanopores of graphene are first tested because the cathode is usually a mix of sulfur and carbon. Then, MoS 2 and Mo-doped graphene are evaluated because of the well-known Mo–S affinity. Finally, a material which has been reported successful in experimental studies, MnO 2 , is analyzed and compared with another oxide surface, Fe 2 O 3 . Adsorption energies of the polysulfides to the surfaces and the detailed interactions of the Li ions and S atoms with the substrate are characterized via charge and geometric analyses. Both the Mo-containing materials and the oxides adsorb the polysulfides much more strongly than graphene nanopores do. However, some of these surfaces are found to be excessively reactive. Thus, a balance between affinity for S and moderate surface reactivity is found as a promising guideline for designing these materials.

25 ENERGY STORAGE↗

DOE OSTI2015

Nanodevices for generating power from molecules and batteryless sensing

A nanoconverter or nanosensor is disclosed capable of directly generating electricity through physisorption interactions with molecules that are dipole containing organic species in a molecule interaction zone. High surface-to-volume ratio semiconductor nanowires or nanotubes (such as ZnO, silicon, carbon, etc.) are grown either aligned or randomly-aligned on a substrate. Epoxy or other nonconductive polymers are used to seal portions of the nanowires or nanotubes to create molecule noninteraction zones. By correlating certain molecule species to voltages generated, a nanosensor may quickly identify which species is detected. Nanoconverters in a series parallel arrangement may be constructed in planar, stacked, or rolled arrays to supply power to nano- and micro-devices without use of external batteries. In some cases breath, from human or other life forms, contain sufficient molecules to power a nanoconverter. A membrane permeable to certain molecules around the molecule interaction zone increases specific molecule nanosensor selectivity response.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2017

Nanodevices for generating power from molecules and batteryless sensing

36 MATERIALS SCIENCE↗

DOE OSTI2015

Serine 363 of a hydrophobic region of Archaeal ribulose 1,5-bisphosphate carboxylase/oxygenase from Archaeoglobus fulgidus and Thermococcus kodakaraensis affects CO 2 /O 2 substrate specificity and oxygen sensitivity

Archaeal ribulose 1, 5-bisphospate carboxylase/oxygenase (RubisCO) is differentiated from other RubisCO enzymes and is classified as a form III enzyme, as opposed to the form I and form II RubisCOs typical of chemoautotrophic bacteria and prokaryotic and eukaryotic phototrophs. The form III enzyme from archaea is particularly interesting as several of these proteins exhibit unusual and reversible sensitivity to molecular oxygen, including the enzyme from Archaeoglobus fulgidus . Previous studies with A. fulgidus RbcL2 had shown the importance of Met-295 in oxygen sensitivity and pointed towards the potential significance of another residue (Ser-363) found in a hydrophobic pocket that is conserved in all RubisCO proteins. In the current study, further structure/function studies have been performed focusing on Ser-363 of A. fulgidus RbcL2; various changes in this and other residues of the hydrophobic pocket point to and definitively establish the importance of Ser-363 with respect to interactions with oxygen. In addition, previous findings had indicated discrepant CO 2 /O 2 specificity determinations of the Thermococcus kodakaraensis RubisCO, a close homolog of A. fulgidus RbcL2. As a result, it is shown here that the T. kodakaraensis enzyme exhibits a similar substrate specificity as the A. fulgidus enzyme and is also oxygen sensitive, with equivalent residues involved in oxygen interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Substrate Engineered Interconnected Graphene Electrodes with Ultrahigh Energy and Power Densities for Energy Storage Applications

Supercapacitors combine the advantages of electrochemical storage technologies like high energy density batteries and high power density capacitors. At 5-10 W h Kg -1 , the energy densities of current supercapacitors are still significantly lower than energy densities of lead acid (20-35 W h Kg -1 ), Ni-metal hydride (40-100 W h Kg -1 ) and Li-ion (120-170 W h Kg -1 ) batteries. Recently, graphene based supercapacitors have shown energy density of 40-80 W h kg -1 . However, their performance is mainly limited due to the reversible agglomeration and restacking of individual graphene layers caused by π-π interactions. The restacking of graphene layers leads to significant decrease of ion-accessible surface area and the low capacitance of graphene based supercapacitors. Here, we introduce a microstructure substrate based method to produce fully delaminated and stable interconnected graphene structure using flash reduction of GO in a few seconds. With this structure, here we achieve the highest amount of volumetric capacitance obtained so far by any type of pure carbon based material. The affordable and scalable production method is capable of producing electrodes with energy density of 0.37 Wh cm -3 and power density of 416.6 W cm -3 . This electrode maintained more than 91 % of its initial capacitance after 5000 cycles. Moreover, combining with ionic liquid, this solvent free graphene electrode material is highly promising for on-chip electronics, micro supercapacitors as well as high power applications.

25 ENERGY STORAGE↗

DOE OSTI2019

Liquid-State Dewetting of Pulsed-Laser-Heated Nanoscale Metal Films and Other Geometries

Metal films of nanoscale thickness, deposited on substrates and exposed to laser heating, provide systems that involve several interesting multiphysics effects. In addition to fluid mechanical aspects associated with a free boundary setup, other relevant physical effects include phase change, thermal flow, and liquid–solid interactions. Such films are challenging to model, in particular because inertial effects may be relevant, and large contact angles require care when considering the long-wave formulation. Applications of nanoscale metal films are numerous, and the materials science community is actively pursuing more complex setups involving templated films and substrates, bimetallic films and alloys, and a variety of elemental film geometries. The goal of this review is to discuss our current understanding of thin metal film systems, while also providing an overview of the challenges in this research area, which stands at the intersection of fluid mechanics, materials science, and thermal physics.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Structural and functional evidence that lipoprotein LpqN supports cell envelope biogenesis in Mycobacterium tuberculosis

The mycobacterial cell envelope is crucial to host–pathogen interactions as a barrier against antibiotics and the host immune response. In addition, cell envelope lipids are mycobacterial virulence factors. Cell envelope lipid biosynthesis is the target of a number of frontline tuberculosis treatments and has been the focus of much research. However, the transport mechanisms by which these lipids reach the mycomembrane remain poorly understood. Many envelope lipids are exported from the cytoplasm to the periplasmic space via the mycobacterial membrane protein large (MmpL) family of proteins. In other bacteria, lipoproteins can contribute to outer membrane biogenesis through direct binding of substrates and/or protein–protein associations with extracytoplasmic biosynthetic enzymes. In this report, we investigate whether the lipoprotein LpqN plays a similar role in mycobacteria. Using a genetic two-hybrid approach, we demonstrate that LpqN interacts with periplasmic loop domains of the MmpL3 and MmpL11 transporters that export mycolic acid–containing cell envelope lipids. We observe that LpqN also interacts with secreted cell envelope biosynthetic enzymes such as Ag85A via pulldown assays. The X-ray crystal structures of LpqN and LpqN bound to dodecyl-trehalose suggest that LpqN directly binds trehalose monomycolate, the MmpL3 and Ag85A substrate. Finally, we observe altered lipid profiles of the ΔlpqN mutant during biofilm maturation, pointing toward a possible physiological role for the protein. The results of this study suggest that LpqN may act as a membrane fusion protein, connecting MmpL transporters with periplasmic proteins, and provide general insight into the role of lipoproteins in Mycobacterium tuberculosis cell envelope biogenesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Influence of Steric and Electronic Properties of P2 Groups on Covalent Inhibitor Binding to SARS-CoV-2 Main Protease

The main protease (MPro) of SARS-CoV-2 is a critical enzyme required for viral replication, making it a prime target for antiviral drug development. Covalent inhibitors, which form a stable interaction with the catalytic C145, have demonstrated strong inhibition of MPro, but the influence of steric and electronic properties of P2 substituents, designed to engage the S2 substrate-binding subsite within the MPro active site, on inhibitor binding affinity remains underexplored. Here, in this study, we design and characterize two hybrid covalent inhibitors, BBH-3 and BBH-4, and present their X-ray crystallographic structures in complex with MPro, providing molecular insights into how their distinct P2 groups, a dichlorobenzyl moiety in BBH-3 and an adamantyl substituent in BBH-4, affect binding conformation and active site adaptability. Comparative structural analyses with previously characterized inhibitors, including BBH-2 and Mcule-5948770040, reveal how the P2 bulkiness and electronic properties influence active site dynamics, particularly through interactions with the S2 and S5 subsites. The P2 group of BBH-3 induces conformational shifts in the S2 helix and the S5 loop, while BBH-4 displaces M49, stabilizing its binding through hydrophobic interactions. Isothermal titration calorimetry further elucidates the impact of P2 modifications on inhibitor affinity, revealing a delicate balance between enthalpic and entropic contributions. The data demonstrate that BBH-3 exhibits less favorable binding, affirming that dichlorobenzyl substitution at the P2 position has a more negative impact on the affinity for MPro than bulky saturated cyclic groups. This underscores the feature that MPro active site malleability may be accompanied by a conformational strain.

SARS-CoV-2↗

DOE OSTI2021

EPS8 supports pancreatic cancer growth by inhibiting BMI1 mediated proteasomal degradation of ALDH7A1

Aldehyde dehydrogenase 7 family member A1 (ALDH7A1) is an enzyme catalyzing lipid peroxidation of fatty aldehydes. It plays a critical role in sustaining high oxygen consumption rate (OCR) and ATP production in pancreatic ductal adenocarcinoma (PADC). However, why PADC cells maintain a relatively high level of ALDH7A1 concentration is still not well understood. In the current study, we explored the interplay between epidermal growth factor receptor kinase substrate 8 (EPS8) and ALDH7A1 in PADC cells. PADC cell lines MIA PaCa-2 and AsPANC-1 were used for in vitro and in vivo studies. The co-IP assay showed mutual interactions between Flag-EPS8 and Myc-ALDH7A1 in both MIA PaCa-2 and AsPANC-1 cells. EPS8 knockdown resulted in decreased ALDH7A1 protein levels and increased poly-ubiquitination. An interaction was observed between ALDH7A1 and BMI1 but not between BMI1 and EPS8. BMI1 knockdown reduced ALDH7A1 poly-ubiquitination and degradation caused by EPS8 knockdown. Dual EPS8 and ALDH7A1 knockdown had a synergistic effect on suppressing PADC cell proliferation in vitro and in vivo. In conclusion, this study revealed that EPS8 supports PADC growth by interacting with ALDH7A1 and inhibiting BMI1 mediated proteasomal degradation of ALDH7A1.

60 APPLIED LIFE SCIENCES↗