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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Formation of Complex Organic Molecules (COMs) from Polycyclic Aromatic Hydrocarbons (PAHs): Top-Down Synthesis of organics in planetary systems

Complex, organic molecules have been found in many solar system objects (i.e., dust, comets, meteorites, moons, etc.); however, their origins and formation remain a mystery. Two chemical evolutionary pathways have been proposed to explain the organic inventory of our solar system. The first pathway, the top-down approach, suggests an interstellar (ISM) heritage whereby the organic material found in the solar system formed from the erosion and functionalization of large pre-solar carbon-bearing species (mainly large Polycyclic Aromatic Hydrocarbons or PAHs). The second pathway suggests that the origin of the Solar System prebiotic matter is the result of bottom-up synthesis from small reactive molecules (e.g., formaldehyde – H2CO, acetylene – H2C2, and similar species). In this second scenario, it is supposed that very few, if any, pre-solar large molecules could have survived due to the proto - solar nebula radiation environment. Polycyclic Aromatic Hydrocarbons or PAHs comprise ~20-30% of all available carbon in the Universe. The PAHs found within our Solar System tend to be smaller than those suspected to be in the ISM, comprised of only 14 to 18 carbon atoms in size whereas ISM PAHs are typically 50 to 100 carbon atoms. The disparity in PAH sizes between the ISM and Solar System environments is not understood, but may point to conversion of large ISM PAHs to Solar System Organics. This presentation details recent experiments regarding the stability of large PAHs to the various types of radiation found within a proto - solar disk and the production of smaller, complex, molecules from the degradation of the larger PAHs. The presentation will highlight differences and similarities in degradation products based on experimental conditions (e.g., radiation type) and discuss future work with a new experimental setup known as ICEE (Institute for Carbon Evolution Experiments).

molecukes↗
NASA NTRS2021

Sulfur Molecules in Space by X-rays: A Computational Study

X-ray astronomy lacks high resolution spectra of interstellar dust analogues and molecules, severely hampering interstellar medium studies based on upcoming X-ray missions. Various theoretical approaches may be used to address this problem, but they must first be shown to reproduce reliable spectra compared to the experiment. In this work, we calculate the sulfur Kedge X-ray absorption spectra of H2S, SO2, and OCS, whose spectra are already known from X-ray experiments and predict the X-ray spectrum of CS, which as far as we are aware has not been measured, thereby hampering its detection by X-ray telescopes. We chose these four molecules as the astrochemistry of sulfur is an unsolved problem and as the four molecules are already known to exist in space. We consider three types of methods for modeling the X-ray spectra: more accurate calculations with the algebraic-diagrammatic construction (ADC) and the CC2, CCSD, and CC3coupled cluster (CC) approaches as well as more affordable ones with transition potential density functional theory (TP-DFT). A comparison of our computational results to previously reported experimental spectra shows that the core−valence separation (CVS)approaches CVS-ADC(2)-x and CVS-CC3 generally yield a good qualitative level of agreement with the experiment, suggesting that they can be used for interpreting measured spectra, while the TP-DFT method is not reliable for these molecules. However, quantitative agreement with the experiment is still outside the reach of the computational methods studied in this work.

Goranka Bilalbegovic↗
NASA NTRSDate not supplied

Active Solar-Like Stars and the Production of Prebiotically Relevant Molecules in Young Earth Like Exoplanet

The magnetic activity of young G type stars produces elevated ionizing radiation fluxes for its planetary system. X-ray, Extreme UV, flare radiation and the associated precipitating energetic particles accelerated in coronal mass ejection driven shocks can drive complex chemistry in the exoplanetary atmosphere, and ignite the production of complex molecules (Airapetian et al., 2016; Hayworth et al. 2021). To address the efficiency of the production of prebiotic molecules in young Earth-like environments, we developed and coupled a set of atmospheric models that account for the determination of the flux of precipitating particle, its ionization/dissociation effects in the planetary atmosphere, and the subsequent chemistry that leads to the creation of prebiotic molecules and greenhouse gases. We show that the productions rates are high enough to provide critical input for the origin of prebiotic molecules on the early Earth. Overall, the impact of the space weather on the atmospheric photochemistry should not be neglected when assessing the factors of habitability of the environments of young rocky (exo)planets.

Guillaume Gronoff↗
NASA NTRS2022

Line Coupling and Line Mixing Effects on Calculated Widths of Symmetric-Top Molecules With the k-Degeneracy: A Theoretical Study of N 2 -, O 2 -, and Air-Broadened Lines of CH 3 I

Calculations of the N 2 -, O 2 - and air-broadened widths, together with their temperature dependence exponents have been made for transitions of CH 3 I in the v 5 and v 6 bands. The calculations are based on a semi-classical line shape formalism developed by the current authors through modifying and refining the Robert-Bonamy formalism. In recent years, we have applied this formalism for linear molecules, symmetric-top molecules with inversion symmetry, and asymmetric-top molecules. For symmetric-top molecules with the k degeneracy such as CH 3 I, the formalism has a new feature. In this case, one should consider each of the CH 3 I transitions labeled by k i or ƒ ≠ 0 as a doublet. Then, one needs to consider the effects of the line mixing process between these two components. Comparisons of our theoretical predictions with some data available demonstrate a very reasonable agreement. Finally we propose new experiments at higher perturber pressures that would enable one to check the theoretically calculated relaxation matrices and to extend the analysis to the interdoublet mixing effects.

Line coupling↗
NASA NTRS2023

Soluble Organic Molecules in Samples of the Carbonaceous Asteroid (162173) Ryugu

The Hayabusa2 spacecraft collected samples from the surface of the carbonaceous near-Earth asteroid (162173) Ryugu, and brought them to Earth. The samples were expected to contain organic molecules, which record processes that occurred in the early Solar System. We analyzed organic molecules extracted from the Ryugu surface samples. We identify a variety of molecules containing the atoms CHNOS, formed by methylation, hydration, hydroxylation, and sulfurization reactions. Amino acids, aliphatic amines, carboxylic acids, polycyclic aromatic hydrocarbons, and nitrogen-heterocyclic compounds were detected, with properties consistent with an abiotic origin. These compounds likely arose from aqueous reaction on Ryugu’s parent body and are similar to organics in Ivuna-type meteorites. These molecules can survive on the surfaces of asteroids and be transported throughout the Solar System.

Hiroshi Naraoka↗
NASA NTRS2024

Primordial Aqueous Alteration Recorded in Water-Soluble Organic Molecules from the Carbonaceous Asteroid (162173) Ryugu

We report primordial aqueous alteration signatures in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu by the Hayabusa2 spacecraft of JAXA. Newly identified low-molecular-weight hydroxy acids (HO-R-COOH) and dicarboxylic acids (HOOC-R-COOH), such as glycolic acid, lactic acid, glyceric acid, oxalic acid, and succinic acid, are predominant in samples from the two touchdown locations at Ryugu. The quantitative and qualitative profiles for the hydrophilic molecules between the two sampling locations shows similar trends within the order of ppb (parts per billion) to ppm (parts per million). A wide variety of structural isomers, including α- and β-hydroxy acids, are observed among the hydrophilic molecules. We also identify pyruvic acid and dihydroxy and tricarboxylic acids, which are biochemically important intermediates relevant to molecular evolution, such as the primordial TCA (tricarboxylic acid) cycle. Here, we find evidence that the asteroid Ryugu samples underwent substantial aqueous alteration, as revealed by the presence of malonic acid during keto–enol tautomerism in the dicarboxylic acid profile. The comprehensive data suggest the presence of a series for water-soluble organic molecules in the regolith of Ryugu and evidence of signatures in coevolutionary aqueous alteration between water and organics in this carbonaceous asteroid.

Asteroids, comets and Kuiper belt↗
DOE OSTI2026

Edge‐Driven Fringe‐Field Effects, Reduced Screening, and Bandgap Widening in Graphene Nanoribbons Enable Single‑Molecule Sensitivity

Graphene nanoribbons (GNRs) offer promising platforms for single‐molecule sensing due to their quasi‐1D channels and discrete electronic states, providing superior sensitivity toward molecular perturbations. While prior studies emphasize smoother edges as essential for optimal performance, the potential benefits of controlled edge roughness remain largely unexplored. Additionally, most investigations focus on GNR arrays, leaving critical edge‐ and width‐dependent factors, including fringe fields, bandgap widening, interactions between adsorbing molecules and GNR atoms, density of states (DOS) suppression, and electrostatic screening lengths, and their collective impact on sensitivity, poorly understood. Here, in this work, we fabricated field‐effect transistors using individual GNRs (widths: 200–20 nm) and characterized their response to molecular adsorption with perfluorooctanoic acid as the model analyte. Narrower ribbons displayed significantly enhanced sensitivity, yielding a coverage‐normalized response of 116 ± 10 mV per molecule in 20 nm‐wide GNRs (from calibrated ensemble Dirac‐point shifts). Experimental and theoretical analyses reveal that this heightened sensitivity arises from stronger fringe fields, width‐dependent quantum confinement effects, reduced DOS, and increased edge roughness that facilitates molecular anchoring, enhanced orbital overlap, and improved charge transfer efficiency. Our findings challenge the conventional assumption that smoother edges inherently enhance sensor performance, demonstrating that controlled edge disorder substantially boosts molecular sensitivity in GNR sensors.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Signatures of Non-universal Quantum Dynamics of Ultracold Chemical Reactions of Polar Alkali Dimer Molecules with Alkali Metal Atoms: Li( 2 S) + NaLi( a 3 Σ + ) → Na( 2 S) + Li 2 ( a 3 Σ u + )

Ultracold chemical reactions of weakly bound triplet-state alkali metal dimer molecules have recently attracted much experimental interest. Here we perform rigorous quantum scattering calculations with a new ab initio potential energy surface to explore the chemical reaction of spin-polarized NaLi(a 3 Σ + ) and Li( 2 S) to form Li 2 (a 3 Σ u + ) and Na( 2 S). The reaction is exothermic and proceeds readily at ultralow temperatures. Significantly, we observe strong sensitivity of the total reaction rate to small variations of the three-body part of the Li 2 Na interaction at short range, which we attribute to a relatively small number of open Li 2 (a 3 Σ u + ) product channels populated in the reaction. This provides the first signature of highly non-universal dynamics seen in rigorous quantum reactive scattering calculations of an ultracold exothermic insertion reaction involving a polar alkali dimer molecule, opening up the possibility of probing microscopic interactions in atom+molecule collision complexes via ultracold reactive scattering experiments.

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

Exploring the scaling limitations of the variational quantum eigensolver with the bond dissociation of hydride diatomic molecules

Abstract Materials simulations involving strongly correlated electrons pose fundamental challenges to state‐of‐the‐art electronic structure methods but are hypothesized to be the ideal use case for quantum computing algorithms. To date, no quantum computer has simulated a molecule of a size and complexity relevant to real‐world applications, despite the fact that the variational quantum eigensolver (VQE) algorithm can predict chemically accurate total energies. Nevertheless, because of the many applications of moderately sized, strongly correlated systems, such as molecular catalysts, the successful use of the VQE stands as an important waypoint in the advancement toward useful chemical modeling on near‐term quantum processors. In this paper, we take a significant step in this direction. We lay out the steps, write, and run parallel code for an (emulated) quantum computer to compute the bond dissociation curves of the TiH, LiH, NaH, and KH diatomic hydride molecules using the VQE. TiH was chosen as a relatively simple chemical system that incorporates d orbitals and strong electron correlation. Because current VQE implementations on existing quantum hardware are limited by qubit error rates, the number of qubits available, and the allowable gate depth, recent studies using it have focused on chemical systems involving s and p block elements. Through VQE + UCCSD calculations of TiH, we evaluate the near‐term feasibility of modeling a molecule with d‐orbitals on real quantum hardware. We demonstrate that the inclusion of d‐orbitals and the use of the UCCSD ansatz, which are both necessary to capture the correct TiH physics, dramatically increase the cost of this problem. We estimate the approximate error rates necessary to model TiH on current quantum computing hardware using VQE + UCCSD and show them to likely be prohibitive until significant improvements in hardware and error correction algorithms are available.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Production of graphene-derivatives using organic molecules for supercapacitors and beyond

Graphene is rapidly expanding for applications ranging from nanoelectronics to space exploration. A material with such enormous potential requires a variety of synthesis methods. Here, we report a library of relatively sustainable redox-active organic molecules for the reduction of graphene oxide (GO) namely N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD), 7,7,8,8-tetracyanoquinodimethane (TCNQ), ferrocene (Ferro), and decamethylferrocene (DFerro). Among them, the reduction of GO using TMPD starts even with simple hand-shaking for just a few minutes. By controlling the sonication time under ambient conditions, one can control the electronic properties of the reduced graphene oxide (rGO). The resulting free-standing films delivered a capacitance of 185 F/g when tested them as supercapacitor electrodes. We also demonstrated that TMPD can exfoliate graphite into few-layer graphene sheets with simple sonication. Here, we further show that under mild heating, these molecules can serve as dopants during the reduction process to produce nitrogen-doped graphene. Our results may guide researchers to explore sustainable organic molecules for the large-scale production of graphene-based materials for diverse applications.

36 MATERIALS SCIENCE↗
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 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↗