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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Effects of Saccharomyces cerevisiae quorum sensing signal molecules on ethanol production in bioethanol fermentation process

Here in this study, the concentrations of Saccharomyces cerevisiae quorum sensing signal molecules (QSMs) were determined, not to mention the exploration of the effects of exogenous S. cerevisiae QSMs on the sole fermentation of S. cerevisiae and co-fermentation of S. cerevisiae and Lactobacillus plantarum. The results showed that the concentrations of three signal molecules (2-phenylethanol (2-PE), tyrosol and tryptophan) produced by S. cerevisiae increased with a higher bacteria density, which tends to become stable up to 118.02, 32.05 and 1.93 mg/L respectively when cultivating for 144 h. Among the three signaling molecules, only 2-PE promoted the ethanol production capacity of S. cerevisiae. The ethanol concentration of the sole fermentation of S. cerevisiae loaded with 120 mg/L 2-PE reached 3.2 g/L in 9 h, which was 58.7% higher than that of the group without 2-PE addition. Moreover, 2-PE reduced the negative impact of L. plantarum on S. cerevisiae. Within 12 h of the co-fermentation of L. plantarum and S. cerevisiae, the ethanol concentration in the co-fermentation group loaded with 2-PE reached 5.6 g/L, similar to that in the group fermenting with sole S. cerevisiae, and the yeast budding rate was also restored to 28.51%. qRT-PCR results of S. cerevisiae which was in sole fermentation with 2-PE addition for 9 h showed that the relative expression levels of ethanol dehydrogenase gene ADH1 in S. cerevisiae decreased by 25% and the relative expression levels of MLS1, CIT2, IDH1,CIT1 decreased by 26%, 30%, 22%,18%, respectively, meant that the glyoxylic and tricarboxylic acid cycles were greatly inhibited, which promotes the accumulation of ethanol. The results of this study provide basic data for using QSMs more than antibiotics in the the prevention of contamination during the industrialized bioethanol production.

2-phenylethanol↗
DOE OSTI2019

Nanoconfinement and Mass Transport in Silica Mesopores: the Role of Charge at the Single Molecule and Single Pore Levels

Polarization-dependent single molecule tracking was employed to simultaneously probe the translational and orientational diffusion of four perylene diimide (PDI) dyes, having different lengths and charges, within the one-dimensional (1D) nanoscale pores of surfactant-templated mesoporous silica films. The wide-field fluorescence videos acquired reveal that a significant fraction of the molecules follow 1D pathways and exhibit highly polarized fluorescence, consistent with their orientational confinement. Single-frame step size distributions prepared from these data were fit to a new model that accurately describes the distribution for 1D Fickian diffusion in the presence of finite localization precision. Average diffusion coefficients obtained from mean square displacement (D MSD ) data were 20–100% larger for the two uncharged PDIs compared to the charged PDIs, reflecting electrostatic interactions of the latter with oppositely charged sites on the cationic surfactant headgroups and deprotonated silanol sites on the pore walls. Polarization-dependent tracking data show that the longest uncharged PDI was most strongly confined, while the three shorter dyes were less confined. The cationic PDI produced a wobbling angle distribution that was broader than the others, suggesting it explores more of the pore diameter. In conclusion, the results provide new knowledge on the mechanisms by which the dye molecules interact with the pore-filling medium and the pore surfaces, helping to elucidate the factors controlling the rate of mass transport.

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

Side Chain and Solvent Direction of Film Morphology in Small-Molecule Organic Solar Materials

Film morphology control is essential to materials development for efficient organic solar cells (OSCs). Unlocking methods to optimize the film morphology for materials without changing the fundamental electronic characteristics can enable previously unacceptable materials to achieve high performance. In this work, a series of acceptor-donor-acceptor (ADA) small molecule p-type OSC semiconductors having benzo[1,2-b:6,5-b0]dithiophene (bBDT) donor units and thiophene capped diketopyrrolopyrrole (TDPP) acceptor units are examined where the sole molecular design variation is in the electronically inactive side chains. Four bBDT(TDPP) 2 compounds with all possible combinations of either 2-ethelhexyl (EH), or 3,7-dimtheyloctyl (DMO) side chains on the bBDT core and TDPP units are discussed. When processed from a chloroform (CF)-only solution, blend films of the molecules with the PC 71 BM electron acceptor exhibit similar thin film properties and photovoltaic performance, regardless of the side chain composition. However, when the additive 1,8-diiodooctane (DIO) is included in the processing solution, the morphological properties and OSC performance diverge dramatically, with the side chain variations now dictating the film morphology, resulting in a >400% spread in power conversion efficiency (PCE). Donor molecules with a mixed side chain motif having the larger DMO side chain on the bBDT core unit deliver the best performance owing to greater donor:acceptor phase intermixing while maintaining contiguous and efficient charge transport pathways. Using in situ GIWAXS during spin-coating, it is shown that DIO extends crystallization times, thereby promoting more thermodynamically driven structures where the side chain compositions have greater impact. Lastly, general guidelines are presented for achieving morphological optimization via combined side chain engineering and processing additives.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Cholesky Decomposition-Based Implementation of Relativistic Two-Component Coupled-Cluster Methods for Medium-Sized Molecules

A Cholesky decomposition (CD)-based implementation of relativistic two-component coupled-cluster (CC) and equation-of-motion CC (EOM-CC) methods using an exact two-component Hamiltonian augmented with atomic-mean-field integrals (the X2CAMF scheme) is reported. Furthermore, the present CD-based implementation of X2CAMF-CC and EOM-CC methods employs atomic-orbital-based algorithms to avoid the construction of two-electron integrals and intermediates involving three and four virtual indices. The CD-based implementation extends the applicability of X2CAMF-CC and EOMCC methods to medium-sized molecules with the correlation of around 1000 spinors. Benchmark calculations for uranium-containing small molecules have been performed to assess the dependence of CC results with respect to the Cholesky threshold. A Cholesky threshold of 10 –4 is shown to maintain chemical accuracy. Example calculations to illustrate the capability of the CD-based relativistic CC methods are reported for the bond dissociation energy of the uranium hexafluoride molecule, UF 6 , with up to quadruple-zeta basis sets and the lowest excitation energy in solvated uranyl ion [UO 2 2+ (H 2 O) 12 ].

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

Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms

Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. Here we find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.

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

Hydration-Induced Disorder Lowers the Energy Barriers for Methyl Rotation in Drug Molecules

The thermally activated dynamics of methyl groups are important for biochemical activity as they allow for a more efficient sampling of the energy landscape. In this work, we compare methyl rotations in the dry and variously hydrated states of three primary drugs under consideration to treat the recent coronavirus disease (COVID-19), namely, hydroxychloroquine and its sulfate, dexamethasone and its sodium diphosphate, and remdesivir. We find that the main driving force behind the considerable reduction in the activation energy for methyl rotations in the hydrated state is the hydration-induced disorder in the methyl group local environments. Furthermore, the activation energy for methyl rotations in the hydration-induced disordered state is much lower than that in an isolated drug molecule, indicating that neither isolated molecules nor periodic crystalline structures can be used to analyze the potential landscape governing the side group dynamics in drug molecules. Instead, only the explicitly considered disordered structures can provide insight.

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

Understanding Fragmentation of Organic Small Molecules in Atom Probe Tomography

In atom probe tomography of molecular organic materials, field ionization of either entire molecules or molecular fragments can occur, but the mechanism governing this behavior was not previously understood. This work explains when a doubly ionized small molecule organic material is expected to undergo fragmentation. Here, we find that multiple detection events arising from post-ionization fragmentation of a parent molecular dication into two daughter ions is well explained by the free energy and geometries of the molecules computed using density functional theory. Of the systems studied, exergonic free energies for formation of the daughter ions, smaller activation energies for dissociation, and increases in bond length are all found to be quantitative predictors for ion fragmentation. This work expands the applicability of atom probe tomography to organic materials by increasing the fundamental understanding of processes occurring during this analysis technique.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Linear Combination of Atomic Dipoles to Calculate the Bond and Molecular Dipole Moments of Molecules and Molecular Liquids

Here we report a linear combination of atomic dipole (LCAD) method for calculating the bond dipole moments of molecules. We show that the LCAD method reproduces the known molecular dipole moments of small to large molecules with a small error with respect to experimental and benchmark ab initio calculations, and molecular dipole distributions of bulk water that agree with maximally localized Wannier functions. The bond dipole moments derived from LCAD are also chemically interpretable in terms of the trend in bond ionicity in going from neutral to charged molecules. Moreover, the LCAD method accurately captures the influence of electric fields, supported by the correct trend in the change of the dipole moment under a uniform external electric field. The better grounding of bond dipole calculations indicates that it should also serve as a useful approach to bond dipole-field models used in catalysis or to reconstruct the small dipole of a H-terminated graphene flake.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

New Perspective on Electron Transfer through Molecules

Motivated by experiments which display unusual length and temperature effects for electron transfer in the nanometer length regime, we propose a new approach for describing long range electron transfer (ET) processes through molecules. We posit that the electron reorganization in the molecules (e.g., the electronic polarization of a macromolecule or organic film by an applied electric potential, or the injected charge generating a dipole moment) should be included in the description. We numerically solve a one-dimensional model for the electron transport, which includes electron-electron interactions explicitly; and we show that it generates a power law distance dependence for electron similar to that observed in experiments. The model does not include vibrations explicitly and should be consistent with the weak temperature dependences observed experimentally. This approach emphasizes the need to treat the electronic changes in the molecule(s) more explicitly to understand the behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Optically Addressing Circularly Polarized Vibrations in Molecules

Circularly polarized (CP) vibrations are the nuclear-motion analog of CP light, emerging in molecules with non-Abelian point-group symmetry that support orthogonal and degenerate vibrational normal modes. Here, in this work, we theoretically explore the optical addressability of CP vibrations, motivated by their potential as nanoscale angular momentum states suitable for information storage and manipulation. We investigate how symmetry-breaking chemical modifications affect a molecule’s capacity to support CP vibrations. Notably, we find cases where modes retain their orthogonality and degeneracy in spite of such modifications, broadening the opportunities afforded by CP vibrations beyond non-Abelian point-group molecules. Prospects for experimental implementations using CP pump–probe techniques are briefly discussed.

group theory↗
DOE OSTI2024

Localized Plasmonic Heating for Single-Molecule DNA Rupture Measurements in Optical Tweezers

To date, studies on the thermodynamic and kinetic processes that underlie biological function and nanomachine actuation in biological- and biology-inspired molecular constructs have primarily focused on photothermal heating of ensemble systems, highlighting the need for probes that are localized within the molecular construct and capable of resolving single-molecule response. Here we present an experimental demonstration of wavelength-selective, localized heating at the single-molecule level using the surface plasmon resonance of a 15 nm gold nanoparticle (AuNP). Our approach is compatible with force-spectroscopy measurements and can be applied to studies of the single-molecule thermodynamic properties of DNA origami nanomachines as well as biomolecular complexes. We further demonstrate wavelength selectivity and establish the temperature dependence of the reaction coordinate for base-pair disruption in the shear-rupture geometry, demonstrating the utility and flexibility of this approach for both fundamental studies of local (nanometer-scale) temperature gradients and rapid and multiplexed nanomachine actuation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

Cofacial Versus Coplanar Arrangement in Centrosymmetric Packing Dimers of Dipolar Small Molecules: Structural Effects on the Crystallization Behaviors and Optoelectronic Characteristics

Two D-π–A-A molecules ( MIDTP and TIDTP ) composed of an electron-rich ditolylamino group (D) and an electron-deficient 5-dicyanovinylenylpyrimidine (A-A) fragment bridged together with indeno[1,2- b ]thiophene (IDT) were synthesized. These molecules provide an opportunity to examine in-depth the impact of side-chain variations (methyl vs p -tolyl) on the crystallization behaviors, solid-state morphology, physical properties, and optoelectronic characteristics relevant for practical applications. X-ray analyses on single-crystal structures indicate that methyl-substituted MIDTP forms “coplanar antiparallel dimers” via C–H···S interactions and organizes into an ordered slip-staircase arrays. In contrast, p -tolyl-bearing TIDTP shows “cofacial centrosymmetric dimers” via π–π interactions and packs into a less-ordered layered structures. The X-ray diffraction analyses upon thermal treatment are consistent with a superior crystallinity of MIDTP , as compared to that of TIDTP . This difference indicates a greater propensity to organization by introduction of the smaller methyl group versus the bulkier p -tolyl group. The increased propensity for order by MIDTP facilitates the crystallization of MIDTP in both solution-processed and vacuum-deposited thin films. MIDTP forms solution-processed single-crystal arrays that deliver OFET hole mobility of 6.56 × 10 –4 cm 2 V –1 s –1 , whereas TIDTP only forms amorhpous films that gave lower hole mobility of 1.34 × 10 –5 cm 2 V –1 s –1 . MIDTP and TIDTP were utilized to serve as donors together with C 70 as acceptor in the fabrication of small-molecule organic solar cells (SMOSCs) with planar heterojunction (PHJ) or planar-mixed heterojunction (PMHJ) device architectures. OPV devices based on higher crystalline MIDTP delivered power conversion efficiencies (PCEs) of 2.5% and 4.3% for PHJ and PMHJ device, respectively, which are higher than those of TIDTP -based cells. Finally, the improved PCEs of MIDTP -based devices are attributed to better hole-transport character.

36 MATERIALS SCIENCE↗
DOE OSTI2024

When Photoelectrons Meet Gas Molecules: Determining the Role of Inelastic Scattering in Ambient Pressure X-ray Photoelectron Spectroscopy

Inelastic photoelectron scattering (IPES) by gas molecules, a critical phenomenon observed in ambient pressure X-ray photoelectron spectroscopy (APXPS), complicates spectral interpretation due to kinetic energy loss in the primary spectrum and the appearance of additional features at higher binding energies. In this study, we systematically investigate IPES in various gas environments using APXPS, providing detailed insights into interactions between photoelectrons emitted from solid surfaces and surrounding gas molecules. Corelevel XPS spectra of Au, Ag, Zn, and Cu metals were recorded over a wide kinetic energy range in the presence of CO 2 , N 2 , Ar, and H 2 gases, demonstrating the universal nature of IPES across different systems. Additionally, we analyzed spectra of scattering effects induced by gas-phase interactions without metal solids. In two reported CO 2 -reduction systems (p-GaN/ Au/Cu and p-Si/TaO x /Cu), we elucidated that IPES is independent of the composition, structure, or size of the solid materials. Using metal foil platforms, we further developed an analytical model to extract electron excitation cross sections of gas molecules. These findings enhance our understanding of IPES mechanisms and enable the predictions of IPES structures in other solid–gas systems, providing a valuable reference for future APXPS studies and improving the accuracy of spectral analysis in gas-rich catalytic interfaces.

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

Covalent Protein Labeling and Improved Single-Molecule Optical Properties of Aqueous CdSe/CdS Quantum Dots

Semiconductor quantum dots (QDs) have proven to be superior probes for single-molecule imaging compared to organic or genetically encoded fluorophores, but they are limited by difficulties in protein targeting, their larger size, and on-off blinking. We report compact aqueous CdSe/CdS QDs with significantly improved bioconjugation efficiency and superior single-molecule optical properties. We have synthesized covalent protein labeling ligands (i.e., SNAP tags) that are optimized for nanoparticle use, and QDs functionalized with these ligands label SNAP-tagged proteins ~10-fold more efficiently than existing SNAP ligands. Single-molecule analysis of these QDs shows 99% of time spent in the fluorescent on-state, ~4-fold higher quantum efficiency than standard CdSe/ZnS QDs, and 350 million photons detected before photobleaching. Bright signals of these QDs enable us to track the stepping movement of a kinesin motor in vitro, and the improved labeling efficiency enables tracking of single kinesins in live cells.

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

Single Molecule Tracking Studies of Lower Critical Solution Temperature Transition Behavior in Poly( N -isopropylacrylamide)

Spatial and temporal heterogeneities in expanded and collapsed surface bound poly(N-isopropylacrylamide), pNIPAAm, films are studied by single molecule tracking (SMT) experiments. Tracking data are analyzed using both radius of gyration (R g ) evolution and confinement level calculations to elucidate the range of behaviors displayed by single Rhodamine6G (R6G) molecules. Furthermore, confined diffusion that is dictated by the free volume within surface tethered chains is observed with considerable dispersion among individual R6G molecules. Thus, the distribution of probe behavior reflects nanometer-scale information about the behavior of the probe–polymer system at temperatures above (T > T LCST ) and below (T < T LCST ) the lower critical solution temperature (LCST). In this context, confinement-level analysis and R g evolution both show a larger degree of confinement of the probe in pNIPAAm at T > T LCST . Temperature-dependent changes in confinement are evidenced at T > T LCST by a higher percentage of confined steps, longer periods of confined events, and smaller area of confined zones, as well as a shift in the overall distribution of R g evolution paths and final R g distributions.

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

Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations

The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Angular and energy distribution of fragment ions in dissociative double photoionization of acetylene molecules at 39 eV

The two-body dissociation reactions of the dication, C{sub 2}H{sub 2}{sup 2+}, produced by 39.0 eV double photoionization of acetylene molecules, have been studied by coupling photoelectron-photoion-photoion coincidence and ion imaging techniques. The results provide the kinetic energy and angular distributions of product ions. The analysis of the results indicates that the dissociation leading to C{sub 2}H{sup +}+H{sup +} products occurs through a metastable dication with a lifetime of 108 {+-} 22 ns, and a kinetic energy release (KER) distribution exhibiting a maximum at {approx}4.3 eV with a full width at half maximum (FWHM) of about 60%. The reaction leading to CH{sub 2}{sup +}+C{sup +} occurs in a time shorter than the typical rotational period of the acetylene molecules (of the order of 10{sup -12} s). The KER distribution of product ions for this reaction, exhibits a maximum at {approx}4.5 eV with a FWHM of about 28%. The symmetric dissociation, leading to CH{sup +} + CH{sup +}, exhibits a KER distribution with a maximum at {approx}5.2 eV with a FWHM of 44%. For the first two reactions the angular distributions of ion products also indicate that the double photoionization of acetylene occurs when the neutral molecule is mainly oriented perpendicularly to the light polarization vector.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Electronic structure of Fe- vs. Ru-based dye molecules

In order to explore whether Ru can be replaced by inexpensive Fe in dye molecules for solar cells, the differences in the electronic structure of Fe- and Ru-based dyes are investigated by X-ray absorption spectroscopy and first-principles calculations. Molecules with the metal in a sixfold, octahedral N cage, such as tris(bipyridines) and tris(phenanthrolines), exhibit a systematic downward shift of the N 1s-to-{pi}* transition when Ru is replaced by Fe. This shift is explained by an extra transfer of negative charge from the metal to the N ligands in the case of Fe, which reduces the binding energy of the N 1s core level. The C 1s-to-{pi}* transitions show the opposite trend, with an increase in the transition energy when replacing Ru by Fe. Molecules with the metal in a fourfold, planar N cage (porphyrins) exhibit a more complex behavior due to a subtle competition between the crystal field, axial ligands, and the 2+ vs. 3+ oxidation states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗