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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 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

A Coincidence Velocity Map Imaging Spectrometer for Ions and High-Energy Electrons to Study Inner-Shell Photoionization of Gas-Phase Molecules

We report on the design and performance of a double-sided coincidence velocity map imaging spectrometer optimized for electron-ion and ion-ion coincidence experiments studying inner-shell photoionization of gas-phase molecules with soft X-ray synchrotron radiation. The apparatus employs two microchannel plate detectors equipped with delay-line anodes for coincident, time- and position-resolved detection of photoelectrons and Auger electrons with kinetic energies up to 300 eV on one side of the spectrometer and photoions up to 25 eV per unit charge on the opposite side. We demonstrate its capabilities by measuring valence photoelectrons and ion spectra of neon and nitrogen and by studying channel-resolved photoelectron and Auger spectra along with fragment-ion momentum correlations for chlorine 2 p inner-shell ionization of cis - and trans -1,2-dichloroethene.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Non-adiabatic molecular dynamics of molecules in the presence of strong light-matter interactions

When the interaction between a molecular system and confined light modes in an optical or plasmonic cavity is strong enough to overcome the dissipative process, hybrid light-matter states (polaritons) become the fundamental excitations in the system. The mixing between the light and matter characters modifies the photophysical and photochemical properties. Notably, it was reported that these polaritons can be employed to control photochemical reactions, charge and energy transfer, and other processes. In addition, according to recent studies, vibrational strong coupling can be employed to resonantly enhance the thermally-activated chemical reactions. In this work, a theoretical model and an efficient numerical method for studying the dynamics of molecules strongly interacting with quantum light are developed based on nonadiabatic excited-state molecular dynamics. The methodology was employed to study the cis-trans photoisomerization of a realistic molecule in a cavity. Numerical simulations demonstrate that the photochemical reactions can be controlled by tuning the properties of the cavity. In the calculated example, the isomerization is suppressed when polaritonic states develop a local minimum on the lower polaritonic state. Moreover, the observed reduction of isomerization is tunable via the photon energy and light-molecule coupling strength. However, the fluctuation in the transition dipole screens the effect of light-matter, which makes it harder to tune the photochemical properties via the coupling strength. These insights gained from this study suggest quantum control of photochemical reactions is possible by specially designed photonic or plasmonic cavities.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Vibrationally resolved photoelectron spectroscopy of oligothiophene radical anions

Vibrationally resolved photoelectron spectroscopy of terthiophene, quaterthiophene, and quinquethiophene radical anions is presented. The increased spectral resolution afforded by the combination of slow photoelectron velocity-map imaging and ion cooling in a cryogenic ion trap allows the characterization of vibronic structures within the S0 and T1 states. Analysis of the spectra, aided by electronic structure calculations and Franck-Condon simulations, revealed evidence for significant contributions from kinetically trapped higher energy conformers in the anion-to-triplet transitions. Unlike the lowest energy structures, where all the thiophene linkers are in the trans configuration, these higher energy conformers contain at least one cis linker. We also found that the adiabatic Franck-Condon simulations drastically underestimated the intensities of some vibronic features in the singlet ground state spectra due to large geometry changes upon photodetachment and anharmonic couplings in the singlet state.

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

Effect of an external electric field on the dynamics and intramolecular structures of ions in an ionic liquid

Simulations of the ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide in an external electric field have been performed using a Drude particle polarizable force field. The structure of the ions has been analyzed, with close attention paid to the configurations of the ions. The “charge arm” concept is used to explain certain changes of these configurations that would be difficult to rationalize otherwise, e.g., trans → cis isomerization of the bis(trifluoromethylsulfonyl)imide anion and extension of the alkyl chain of the cation. It has also been shown that the ions orient themselves so that their charge arms align with and stretch out along the field, and these effects occur at lower external electric field strengths than cause a change in the inherent diffusion of the ions. Here, the dynamics of the system parallel and perpendicular to the field were analyzed, and it was found that the applied field affected the diffusion normal to the field. This is explained as a secondary effect of a change in the ion cage formed by the surrounding counterions of a given ion in the ionic liquid. The breakdown of the ion cages was rationalized by correlating changes to the inherent diffusion of the ions with other changes to the diffusion and bulk structure of the liquid, as well as considering the average forces on the ions compared to the force the ions would be expected to experience in an electric field. Parallel to the field, a drift was observed at every electric field studied. In electric fields with no changes to the ion cage structure, the relationship between the drift and electric field was found to be linear, becoming nonlinear as the ion cage structure breaks down.

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

The pH-dependent orientation of N3 dye on a gold substrate is revealed using heterodyne-detected vibrational sum frequency generation spectroscopy

We report on systematic changes to the adsorption geometry of the dye N3 {[cis-bis(isothiocyanato)bis(2,2' -bipyridyl-4,4' -dicarboxylato ruthenium(II)]} on a gold substrate as the pH of the deposition environment is altered. The protonation states of the four --COOH groups of the N3 dye change according to the modified pH conditions, thus affecting the number of --COOH and --NCS functional groups that participate in the adsorption to gold. Here, we use heterodyne detected vibrational sum frequency generation (HD-VSFG) spectroscopy to obtain surface specific vibrational information on both --COOH and --NCS groups as a function of pH of the deposition conditions. Polarization-dependent HD-VSFG yields sets of complex χ (2) spectra, enabling us to perform a simultaneous fitting procedure to the polarization-dependent real and imaginary components and thus extract detailed structural information of the N3/gold interface. Overall, our results show that N3 preferentially adsorbs to gold either with two --COOH groups and one --NCS group in more acidic conditions or with one --COOH group and two --NCS groups in more basic conditions.

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

Hidden singularities in spontaneously polarized molecular solids

Films of dipolar molecules formed by physical vapor deposition are, in general, spontaneously polarized, with implications ranging from electron transfer in molecular optoelectronic devices to the properties of astrochemical ices in the interstellar medium. Polarization arises from dipole orientation, which should intuitively decrease with increasing deposition temperature, T. However, it is experimentally found that minimum or maximum values in polarization vs T may be observed for cis-methyl formate, 1-propanol, and ammonia. A continuous analytic form of polarization vs T is developed, which has the property that it is not differentiable at all T. The minima and maxima in polarization vs T are marked by singularities in the differential of this analytic form. In conclusion, this exotic behavior is presently unique to films of dipolar species and has not been reported, for example, in the related magnetic phases of spin glasses.

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

Time-resolved vacuum-ultraviolet photoelectron spectroscopy of the à 1 A u state of acetylene

Ultrafast time-resolved photoelectron spectra are reported for the vacuum-ultraviolet (VUV) photoionization of acetylene following excitation to the à 1 A u state via UV absorption at 200 nm. The excitation energy lies above the lowest dissociation threshold to C 2 H X̃ 2 Σ + + H, as well as above the threshold for adiabatic dissociation of the à 1 A u state to form C 2 H (à 2 Π) + H. The time-dependent mass spectra and photoelectron spectra provide insight into the intramolecular decay processes of the à 1 A u state. In addition, photoelectron spectra of the à 1 A u state with VUV light access both the X̃ 2 Π u and à 2 Σ g + states of the ion, as well as the predicted, but previously unobserved, 1 2 Π g state, which corresponds to a two-hole, one-particle configuration that lies in close proximity to the à 2 Σ g + state. The 1 2 Π g state is split into 2 A 2 + 2 B 2 and 2 A g + 2 B g states in the cis and trans configurations, respectively. In conclusion, electronic structure calculations, along with trajectory calculations, reproduce the principal features of the experimental data and confirm the assignment of the 1 2 Π g state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Photoinduced translational molecular mobility in solid nanostructured azo dye films

A new mechanism controlling the molecular motion in thin azo-containing films during a photoinduced change in the surface nanorelief is found. It is shown experimentally that exposure of a solid AD-1 azo dye, deposited on a glass substrate, to incoherent linearly polarised light leads to formation of nanostructures with a characteristic size of 200 nm, which are similar to droplets of melt of this dye on the same substrate. It is shown that photoinduced mass transport in a solid AD-1 azo dye film can be explained by the mobility of molecules related to their trans-cis-photoisomerisation, which leads to film softening with subsequent formation of spherical protrusions under surface tension forces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism

Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions1-3. Different families of enzymes, known as peptidyl-prolyl isomerases (PPIases), catalyse this reaction, which involves the interconversion between the cis and trans isomers of the Nterminal amide bond of the amino acid proline2,3. A complete description of the mechanisms by which these enzymes function, however, has remained elusive. Here, we show that cyclophilin A, one of the most common PPIases4, provides a catalytic environment that acts on the substrate through an electrostatic lever mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carboxylic group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. This mechanism resulted from the analysis of an ensemble of conformations populated by cyclophilin A during the enzymatic reaction using a combination of NMR measurements, molecular dynamics simulations and density functional theory calculations. We anticipate that this approach will be helpful in elucidating whether the electrostatic lever mechanism that we describe is common to other PPIases, and more generally to characterise other enzymatic processes.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2014

Structure of a PE-PPE-EspG complex from Mycobacterium tuberculosis reveals molecular specificity of ESX protein secretion

Nearly 10% of the coding capacity of the Mycobacterium tuberculosis genome is devoted to two highly expanded and enigmatic protein families called PE and PPE, some of which are important virulence/immunogenicity factors and are secreted during infection via a unique alternative secretory system termed "type VII." How PE-PPE proteins function during infection and how they are translocated to the bacterial surface through the five distinct type VII secretion systems [ESAT-6 secretion system (ESX)] of M. tuberculosis is poorly understood. Here in this paper, we report the crystal structure of a PE-PPE heterodimer bound to ESX secretion-associated protein G (EspG), which adopts a novel fold. This PE-PPE-EspG complex, along with structures of two additional EspGs, suggests that EspG acts as an adaptor that recognizes specific PE-PPE protein complexes via extensive interactions with PPE domains, and delivers them to ESX machinery for secretion. Surprisingly, secretion of most PE-PPE proteins in M. tuberculosis is likely mediated by EspG from the ESX-5 system, underscoring the importance of ESX-5 in mycobacterial pathogenesis. Furthermore, our results indicate that PE-PPE domains function as cis -acting targeting sequences that are read out by EspGs, revealing the molecular specificity for secretion through distinct ESX pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Diverse oligomeric states of CEACAM IgV domains

Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) comprise a large family of cell surface adhesion molecules that bind to themselves and other family members to carry out numerous cellular functions, including proliferation, signaling, differentiation, tumor suppression, and survival. They also play diverse and significant roles in immunity and infection. The formation of CEACAM oligomers is caused predominantly by interactions between their N-terminal IgV domains. Although X-ray crystal structures of CEACAM IgV domain homodimers have been described, how CEACAMs form heterodimers or remain monomers is poorly understood. To address this key aspect of CEACAM function, we determined in this paper the crystal structures of IgV domains that form a homodimeric CEACAM6 complex, monomeric CEACAM8, and a heterodimeric CEACAM6–CEACAM8 complex. To confirm and quantify these interactions in solution, we used analytical ultracentrifugation to measure the dimerization constants of CEACAM homodimers and isothermal titration calorimetry to determine the thermodynamic parameters and binding affinities of CEACAM heterodimers. We found the CEACAM6–CEACAM8 heterodimeric state to be substantially favored energetically relative to the CEACAM6 homodimer. Finally, our data provide a molecular basis for the adoption of the diverse oligomeric states known to exist for CEACAMs and suggest ways in which CEACAM6 and CEACAM8 regulate the biological functions of one another, as well as of additional CEACAMs with which they interact, both in cis and in trans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

E-cadherin junction formation involves an active kinetic nucleation process

Epithelial (E)-cadherin-mediated cell–cell junctions play important roles in the development and maintenance of tissue structure in multicellular organisms. E-cadherin adhesion is thus a key element of the cellular microenvironment that provides both mechanical and biochemical signaling inputs. Here, we report in vitro reconstitution of junction-like structures between native E-cadherin in living cells and the extracellular domain of E-cadherin in a supported membrane. Junction formation in this hybrid live cell-supported membrane configuration requires both active processes within the living cell and a supported membrane with low E-cad-ECD mobility. The hybrid junctions recruit α-catenin and exhibit remodeled cortical actin. Observations suggest that the initial stages of junction formation in this hybrid system depend on the trans but not the cis interactions between E-cadherin molecules, and proceed via a nucleation process in which protrusion and retraction of filopodia play a key role.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Mitochondrial Hsp90 is a ligand-activated molecular chaperone coupling ATP binding to dimer closure through a coiled-coil intermediate

Heat-shock protein of 90 kDa (Hsp90) is an essential molecular chaperone that adopts different 3D structures associated with distinct nucleotide states: a wide-open, V-shaped dimer in the apo state and a twisted, N-terminally closed dimer with ATP. Although the N domain is known to mediate ATP binding, how Hsp90 senses the bound nucleotide and facilitates dimer closure remains unclear. In this paper we present atomic structures of human mitochondrial Hsp90 N (TRAP1 N ) and a composite model of intact TRAP1 revealing a previously unobserved coiled-coil dimer conformation that may precede dimer closure and is conserved in intact TRAP1 in solution. Our structure suggests that TRAP1 normally exists in an autoinhibited state with the ATP lid bound to the nucleotide-binding pocket. ATP binding displaces the ATP lid that signals the cis-bound ATP status to the neighboring subunit in a highly cooperative manner compatible with the coiled-coil intermediate state. We propose that TRAP1 is a ligand-activated molecular chaperone, which couples ATP binding to dramatic changes in local structure required for protein folding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Stabilizing a different cyclooctatetraene stereoisomer

Significance Cyclooctatetraene (COT) is a poster child for nonaromatic molecules. An isomer of tub-shaped COT, with one of the ring double bonds changed from the usual cis form to a trans one, lies some 23 kcal/mol higher in energy. Devising a substitution strategy for turning the tables, making the trans isomer the stable point of the system, is the challenge. Simple bonding ideas, of the bulk of substituents, of clamping and turning aromaticity on and off, of pushing electrons in and out of the system, guide us in devising several realistic candidates. Along the way, a set of molecules that might easily split hydrogen reversibly emerges.

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

Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions

Significance Commonly observed secondary structures of proteins, such as α -helices and β -sheets, are built from a trans- amide backbone with residues sampling a single region of the Ramachandran plot. Here we report a secondary structure displayed by biomimetic peptoid polymers in which the backbone exhibits the cis conformation and alternating residues display rotational states of opposed (pseudo)chirality. This structure is linear and untwisted and enables strands to pack densely into extended bilayer nanosheets.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Light-triggered thermal conductivity switching in azobenzene polymers

Materials that can be switched between low and high thermal conductivity states would advance the control and conversion of thermal energy. Employing in situ time-domain thermoreflectance (TDTR) and in situ synchrotron X-ray scattering, we report a reversible, light-responsive azobenzene polymer that switches between high (0.35 W m –1 K –1 ) and low thermal conductivity (0.10 W m –1 K –1 ) states. This threefold change in the thermal conductivity is achieved by modulation of chain alignment resulted from the conformational transition between planar ( trans ) and nonplanar ( cis ) azobenzene groups under UV and green light illumination. This conformational transition leads to changes in the π-π stacking geometry and drives the crystal-to-liquid transition, which is fully reversible and occurs on a time scale of tens of seconds at room temperature. Furthermore this result demonstrates an effective control of the thermophysical properties of polymers by modulating interchain π-π networks by light.

36 MATERIALS SCIENCE↗
DOE OSTI2019

The constrained architecture of mammalian Hox gene clusters

In many animal species with a bilateral symmetry, Hox genes are clustered either at one or at several genomic loci. This organization has a functional relevance, as the transcriptional control applied to each gene depends upon its relative position within the gene cluster. It was previously noted that vertebrate Hox clusters display a much higher level of genomic organization than their invertebrate counterparts. The former are always more compact than the latter, they are generally devoid of repeats and of interspersed genes, and all genes are transcribed by the same DNA strand, suggesting that particular factors constrained these clusters toward a tighter structure during the evolution of the vertebrate lineage. Here, we investigate the importance of uniform transcriptional orientation by engineering several alleles within the HoxD cluster, such as to invert one or several transcription units, with or without a neighboring CTCF site. We observe that the association between the tight structure of mammalian Hox clusters and their regulation makes inversions likely detrimental to the proper implementation of this complex genetic system. We propose that the consolidation of Hox clusters in vertebrates, including transcriptional polarity, evolved in conjunction with the emergence of global gene regulation via the flanking regulatory landscapes, to optimize a coordinated response of selected subsets of target genes in cis .

59 BASIC BIOLOGICAL SCIENCES↗