Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “INTERMEDIATE STATE”

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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

The structure of liquid carbon elucidated by in situ X-ray diffraction

Carbon has a central role in biology and organic chemistry, and its solid allotropes provide the basis of much of our modern technology. However, the liquid form of carbon remains nearly uncharted, and the structure of liquid carbon and most of its physical properties are essentially unknown. But liquid carbon is relevant for modelling planetary interiors and the atmospheres of white dwarfs, as an intermediate state for the synthesis of advanced carbon materials, inertial confinement fusion implosions, hypervelocity impact events on carbon materials and our general understanding of structured fluids at extreme conditions. Here we present a precise structure measurement of liquid carbon at pressures of around 1 million atmospheres obtained by in situ X-ray diffraction at an X-ray free-electron laser. Our results show a complex fluid with transient bonding and approximately four nearest neighbours on average, in agreement with quantum molecular dynamics simulations. The obtained data substantiate the understanding of the liquid state of one of the most abundant elements in the universe and can test models of the melting line. The demonstrated experimental abilities open the path to performing similar studies of the structure of liquids composed of light elements at extreme conditions.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Structure of an allosteric modulator bound to the CB1 cannabinoid receptor

The CB1 receptor mediates the central nervous system response to cannabinoids, and is a drug target for pain, anxiety and seizures. CB1 also responds to allosteric modulators, which influence cannabinoid binding and efficacy. To understand the mechanism of these compounds, we solved the crystal structure of CB1 with the negative allosteric modulator (NAM) ORG27569 and the agonist CP55940. The structure reveals that the NAM binds to an extrahelical site within the inner leaflet of the membrane, which overlaps with a conserved site of cholesterol interaction in many G protein-coupled receptors (GPCRs). The ternary structure with ORG27569 and CP55940 captures an intermediate state of the receptor, in which aromatic residues at the base of the agonist-binding pocket adopt an inactive conformation despite the large contraction of the orthosteric pocket. The structure illustrates a potential strategy for drug modulation of CB1 and other class A GPCRs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Design of two-photon molecular tandem architectures for solar cells by ab initio theory

An extensive database of spectroscopic properties of molecules from ab initio calculations is used to design molecular complexes for use in tandem solar cells that convert two photons into a single electron–hole pair, thereby increasing the output voltage while covering a wider spectral range. Three different architectures are considered: the first two involve a complex consisting of two dye molecules with appropriately matched frontier orbitals, connected by a molecular diode. Optimized combinations of dye molecules are determined by taking advantage of our computational database of the structural and energetic properties of several thousand porphyrin dyes. The third design is a molecular analogy of the intermediate band solar cell, and involves a single dye molecule with strong intersystem crossing to ensure a long lifetime of the intermediate state. Based on the calculated energy levels and molecular orbitals, energy diagrams are presented for the individual steps in the operation of such tandem solar cells. We find that theoretical open circuit voltages of up to 1.8 V can be achieved using these tandem designs. Questions about the practical implementation of prototypical devices, such as the synthesis of the tandem molecules and potential loss mechanisms, are addressed.

14 SOLAR ENERGY↗
DOE OSTI2019

Quantum interferences among Dexter energy transfer pathways

Dexter energy transfer in chemical systems moves an exciton (i.e., an electron–hole pair) from a donor chromophore to an acceptor chromophore through a bridge by a combination of bonded and non-bonded interactions. The transition is enabled by both one-electron/one-particle and two-electron/two-particle interaction mechanisms. Assuming that there is no real intermediate state population of an electron, hole, or exciton in the bridge, the transport involves two states that are coupled non-adiabatically. As such, coherent quantum interferences arise among the Dexter energy coupling pathways. These interferences, while related to well understood interferences in single-electron transfer, are much richer because of their two particle nature: the transfer of a triplet exciton involves the net transfer of both an electron and a hole. Despite this additional complexity, simple rules can govern Dexter coupling pathway interferences in special cases. As in the case of single-electron transfer, identical parallel coupling pathways can be constructively interfering and may enhance the Dexter transfer rate. Because of the virtual particle combinatorics associated with two-particle superexchange, two parallel Dexter coupling routes may be expected to enhance Dexter couplings by more than a factor of two. Here we explore Dexter coupling pathway interferences in non-covalent assemblies, employing a method that enables the assessment of Dexter coupling pathway strengths and interferences, in the context of one-particle and two-particle coupling interactions.

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

Probing radical–molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals

Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical–molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical–molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A “polarize-then-depolarize” (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. The examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical–molecule interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

A complete map of the ion chemistry of the naphthalene radical cation? DFT and RRKM modeling of a complex potential energy surface

The fragmentation mechanisms of the naphthalene molecular ion to [M–C{sub 4}H{sub 2}]{sup +•}, [M–C{sub 2}H{sub 2}]{sup +•}, [M–H{sub 2}]{sup +•}, and [M–H{sup •}]{sup +} were obtained at the UB3LYP/6-311+G(3df,2p)//UB3LYP/6-31G(d) level of theory and were subsequently used to calculate the microcanonical rate constants, k(E)’s, for all the steps by the Rice-Ramsperger-Kassel-Marcus formalism. The pre-equilibrium and steady state approximations were applied on different regions of the potential energy profiles to obtain the fragmentation k(E)’s and calculate the relative abundances of the ions as a function of energy. These results reproduce acceptably well the imaging photoelectron-photoion coincidence spectra of naphthalene, in the photon-energy range 14.0–18.8 eV that was previously reported by our group. Prior to dissociation, the molecular ion rapidly equilibrates with a set of isomers that includes the Z- and E-phenylvinylacetylene (PVA) radical cations. The naphthalene ion is the predominant isomer below 10 eV internal energy, with the other isomers remaining at steady state concentrations. Later on, new steady-state intermediates are formed, such as the azulene and 1-phenyl-butatriene radical cations. The naphthalene ion does not eject an H atom directly but eliminates an H{sub 2} molecule in a two-step fragmentation. H{sup •} loss occurs instead from the 1-phenyl-butatriene ion. The PVA ions initiate the ejection of diacetylene (C{sub 4}H{sub 2}) to yield the benzene radical cation. Acetylene elimination yields the pentalene cation at low energies (where it can account for 45.9%–100.0% of the rate constant of this channel), in a three-step mechanism starting from the azulene ion. However, above 7.6 eV, the major [M–C{sub 2}H{sub 2}]{sup +•} structure is the phenylacetylene cation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Transition metal contacts to graphene

Achieving low resistance contacts to graphene is a common concern for graphene device performance and hybrid graphene/metal interconnects. In this work, we have used the circular Transfer Length Method (cTLM) to electrically characterize Ag, Au, Ni, Ti, and Pd as contact metals to graphene. The consistency of the obtained results was verified with the characterization of up to 72 cTLM structures per metal. Within our study, the noble metals Au, Ag and Pd, which form a weaker bond with graphene, are shown to result in lower contact resistance (Rc) values compared to the more reactive Ni and Ti. X-ray Photo Electron Spectroscopy and Transmission Electron Microscopy characterization for the latter have shown the formation of Ti and Ni carbides. Graphene/Pd contacts show a distinct intermediate behavior. The weak carbide formation signature and the low Rc values measured agree with theoretical predictions of an intermediate state of weak chemisorption of Pd on graphene.

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

In situ x-ray diffraction study of polyamorphism in H 2 O under isothermal compression and decompression

Amorphous-amorphous transformations in H 2 O have been studied under rapid isothermal compression and decompression in a diamond anvil cell together with in situ x-ray diffraction measurements using brilliant synchrotron radiation. The experimental pathways provide a density-driven approach for studying polyamorphic relations among low-, high-, and very high-density amorphs (LDA, HDA, VHDA) in a pressure range of 0-3.5 GPa at temperatures of 145-160 K. Our approach using rapid (de) compression allows for studying the polyamorphic transformations at higher temperatures than the conditions previously studied under slow (de) compression or isobaric annealing. Multiple compression-decompression cycles can be integrated with in situ x-ray measurements, thus facilitating the study of repeatability and reversibility of the polyamorphic transformations. Fast in situ x-ray diffraction measurements allow for obtaining detailed insight into the structural changes across polyamorphic transformations regarding the (dis) continuity, reversibility, and possible intermediate forms. As demonstrated at isothermal conditions of 145 K and 155 K, the polyamorphic transformations are characterized by a sharp and reversible LDA-VHDA transformation, with an HDA-like form (referred to as HDA' appearing as an intermediate state. The LDA-VHDA transformation is found to occur in two steps: a discontinuous transition between LDA and HDA' and a continuous change within HDA' involving structural reconfigurations and finally converging to VHDA. Published under license by AIP Publishing.

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

Evolution of structure and dynamics of thermo-reversible nanoparticle gels—A combined XPCS and rheology study

A combined X-ray photon correlation spectroscopy and rheology report is carried out to capture the evolution of structure, fast particle-scale dynamics, and moduli (elastic and loss) at early times of gel formation near the fluid-gel boundary of a suspension of nanoparticles. The system is made up of moderately concentrated suspensions of octadecyl silica in decalin (φ = 0.2) undergoing thermoreversible gelation. Near the gel boundary, the rate of gel formation is very sensitive to changes in attraction strength. Yet, we find that at different attraction strengths, the system goes through identical intermediate states of microscopic and macroscopic behavior, even though the absolute time needed to form a gel varies by orders of magnitude. We identify a single dimensionless time parameter, t w /t g , where t w is the wait time following the quench and t g is the rheologically determined gel time, that captures the similarity in gel formation at a range of attraction strengths. Following a temperature quench below the gel boundary, the system is initially fluidlike and forms diffusive clusters (similar to 8.5 times the particle diameter). After a lag-time, t L , clusters aggregate to form a network like structure which is characterized by the onset of mechanical rigidity and a rapid growth in microscopic relaxation times. At t g , the Baxter parameter obtained from adhesive hard sphere fits of the structure factor attains a constant value corresponding to the theoretical percolation boundary, thus demonstrating that gelation is percolation driven.

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

Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor

Protein–protein binding is key in cellular signaling processes. Molecular dynamics (MD) simulations of protein–protein binding, however, are challenging due to limited timescales. In particular, binding of the medically important G-protein-coupled receptors (GPCRs) with intracellular signaling proteins has not been simulated with MD to date. Here, we report a successful simulation of the binding of a G-protein mimetic nanobody to the M 2 muscarinic GPCR using the robust Gaussian accelerated MD (GaMD) method. Through long-timescale GaMD simulations over 4,500 ns, the nanobody was observed to bind the receptor intracellular G-protein-coupling site, with a minimum rmsd of 2.48 Å in the nanobody core domain compared with the X-ray structure. Binding of the nanobody allosterically closed the orthosteric ligand-binding pocket, being consistent with the recent experimental finding. In the absence of nanobody binding, the receptor orthosteric pocket sampled open and fully open conformations. The GaMD simulations revealed two low-energy intermediate states during nanobody binding to the M 2 receptor. The flexible receptor intracellular loops contribute remarkable electrostatic, polar, and hydrophobic residue interactions in recognition and binding of the nanobody. As a result, these simulations provided important insights into the mechanism of GPCR–nanobody binding and demonstrated the applicability of GaMD in modeling dynamic protein–protein interactions.

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

Mechanism of tRNA-mediated +1 ribosomal frameshifting

Accurate translation of the genetic code is critical to ensure expression of proteins with correct amino acid sequences. Certain tRNAs can cause a shift out of frame (i.e., frameshifting) due to imbalances in tRNA concentrations, lack of tRNA modifications or insertions or deletions in tRNAs (called frameshift suppressors). Here, we determined the structural basis for how frameshift-suppressor tRNA SufA6 (a derivative of tRNA Pro ) reprograms the mRNA frame to translate a 4-nt codon when bound to the bacterial ribosome. After decoding at the aminoacyl (A) site, the crystal structure of the anticodon stem-loop of tRNA SufA6 bound in the peptidyl (P) site reveals ASL conformational changes that allow for recoding into the +1 mRNA frame. Furthermore, a crystal structure of full-length tRNA SufA6 programmed in the P site shows extensive conformational rearrangements of the 30S head and body domains similar to what is observed in a translocation intermediate state containing elongation factor G (EF-G). The 30S movement positions tRNA SufA6 toward the 30S exit (E) site disrupting key 16S rRNA–mRNA interactions that typically define the mRNA frame. In summary, this tRNA-induced 30S domain change in the absence of EF-G causes the ribosome to lose its grip on the mRNA and uncouples the canonical forward movement of the tRNAs during elongation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Vascular K ATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides

Vascular tone is dependent on smooth muscle K ATP channels comprising pore-forming Kir6.1 and regulatory SUR2B subunits, in which mutations cause Cantú syndrome. Unique among K ATP isoforms, they lack spontaneous activity and require Mg-nucleotides for activation. Structural mechanisms underlying these properties are unknown. Here, we determined cryogenic electron microscopy structures of vascular K ATP channels bound to inhibitory ATP and glibenclamide, which differ informatively from similarly determined pancreatic K ATP channel isoform (Kir6.2/SUR1). Unlike SUR1, SUR2B subunits adopt distinct rotational “propeller” and “quatrefoil” geometries surrounding their Kir6.1 core. The glutamate/aspartate-rich linker connecting the two halves of the SUR-ABC core is observed in a quatrefoil-like conformation. Molecular dynamics simulations reveal MgADP-dependent dynamic tripartite interactions between this linker, SUR2B, and Kir6.1. The structures captured implicate a progression of intermediate states between MgADP-free inactivated, and MgADP-bound activated conformations wherein the glutamate/aspartate-rich linker participates as mobile autoinhibitory domain, suggesting a conformational pathway toward K ATP channel activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

β-Subunit Binding Is Sufficient for Ligands to Open the Integrin α IIb β 3 Headpiece

The platelet integrin α IIb β 3 binds to a KQAGDV motif at the fibrinogen γ-chain C terminus and to RGD motifs present in loops in many extracellular matrix proteins. These ligands bind in a groove between the integrin α and β-subunits; the basic Lys or Arg side chain hydrogen bonds to the α IIb -subunit, and the acidic Asp side chain coordinates to a metal ion held by the β 3 -subunit. Ligand binding induces headpiece opening, with conformational change in the β-subunit. During this opening, RGD slides in the ligand-binding pocket toward α IIb , with movement of the βI-domain β1-α1 loop toward α IIb , enabling formation of direct, charged hydrogen bonds between the Arg side chain and α IIb . Here we test whether ligand interactions with β 3 suffice for stable ligand binding and headpiece opening. We find that the AGDV tetrapeptide from KQAGDV binds to the α IIb β 3 headpiece with affinity comparable with the RGDSP peptide from fibronectin. AGDV induced complete headpiece opening in solution as shown by increase in hydrodynamic radius. Soaking of AGDV into closed α IIb β 3 headpiece crystals induced intermediate states similarly to RGDSP. AGDV has very little contact with the α-subunit. Furthermore, as measured by epitope exposure, AGDV, like the fibrinogen γ C-terminal peptide and RGD, caused integrin extension on the cell surface. Thus, pushing by the β 3 -subunit on Asp is sufficient for headpiece opening and ligand sliding, and no pulling by the α IIb subunit on Arg is required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗