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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells

Carboxysomes are protein microcompartments found in cyanobacteria, whose shell encapsulates rubisco at the heart of carbon fixation in the Calvin cycle. Carboxysomes are thought to locally concentrate CO 2 in the shell interior to improve rubisco efficiency through selective metabolite permeability, creating a concentrated catalytic center. However, permeability coefficients have not previously been determined for these gases, or for Calvin-cycle intermediates such as bicarbonate (HCO$^–_3$), 3-phosphoglycerate, or ribulose-1,5-bisphosphate. Starting from a high-resolution cryogenic electron microscopy structure of a synthetic β-carboxysome shell, we perform unbiased all-atom molecular dynamics to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the bacterial microcompartment trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to HCO$^–_3$ relative to CO 2 . To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO 2 -concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics simulations estimate the mean first passage time for CO 2 assimilation in a crowded model carboxysome. Despite a relatively high CO 2 permeability of approximately 10 -2 cm/s across the carboxysome shell, the shell proteins reflect enough CO 2 back toward rubisco that 2,650 CO 2 molecules can be fixed by rubisco for every 1 CO 2 molecule that escapes under typical conditions. The permeabilities determined from all-atom molecular simulation are key inputs into flux modeling, and the insight gained into carbon fixation can facilitate the engineering of carboxysomes and other bacterial microcompartments for multiple applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Modeling bicarbonate formation in an alkaline solution with multi-level quantum mechanics/molecular dynamics simulations

Understanding carbonate speciation and how it may be modulated is essential for the advancement of carbon dioxide (CO 2 ) capture and storage technologies, which often rely on the transformation of CO 2 into carbonate, e.g. via the formation of carbonate minerals. To date, few atomic-level, quantum-mechanics-based simulations have been carried out to characterize how carbonic acid (H 2 CO 3 ) and bicarbonate ($HCO^{-}_{3}$) form in aqueous solution, and how pH affects this process. Recently, Martirez and Carter utilized rare-event sampling density functional theory molecular dynamics simulations in combination with multi-level embedded correlated wavefunction theory, thus accounting for both solvent dynamics and electron correlation accurately, to elucidate the mechanism of H 2 CO 3 formation in neutral solution (J. Am. Chem. Soc., 145, 12561, 2023). Here, we perform a complementary simulation using the same method to map out the energetics of $HCO^{-}_{3}$ formation from dissolved CO 2 in basic solution. We find that, as in H 2 CO 3 formation, including water dynamics is important to obtain an accurate prediction of the energetics for the aforementioned reaction. Furthermore, only with MD did we identify the correct pathway for the reaction, in which water – not hydroxide – acts as the initial nucleophile and only at the transition state does it lose a proton.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Two-body dissociation of formic acid following double ionization by ultrafast laser pulses

We studied the fragmentation of planar formic acid (HCOOH) molecules following their double ionization by intense ultrashort laser pulses. Deuterium tagging (i.e., HCOOD) combined with coincidence momentum imaging measurements of all fragment ions enabled determination of the role of the hydroxyl and carboxyl hydrogen atoms in the breakup. Specifically, we observe a strong preference for the hydroxyl (OD) group to remain intact in a ${\mathrm{HCOOD}}^{2+}{\rightarrow}{\mathrm{OD}}^{+}+{\mathrm{HCO}}^{+}$ fragmentation, which is an order of magnitude more likely than ${\mathrm{OH}}^{+}+{\mathrm{DCO}}^{+}$. An even larger preference for breaking the H-C bond over the O-H bond is observed in the ${\mathrm{H}}^{+}+{\mathrm{DCO}}_{2}^{+}$ and ${\mathrm{D}}^{+}+{\mathrm{HCO}}_{2}^{+}$ deprotonation channels. Bond rearrangement, leading to ${\mathrm{H}}_{2}^{+}$ or ${\mathrm{H}}_{2}{\mathrm{O}}^{+}$ formation, exhibits no isotopic preference. The kinetic-energy-release distributions of the ${\mathrm{OH}}^{+}+{\mathrm{DCO}}^{+}$ and ${\mathrm{O}}^{+}+{\mathrm{H}}_{2}{\mathrm{CO}}^{+}$ breakup channels suggest that more than one process contributes to these final products, although further theoretical work is needed to identify the specific paths.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Carbonate Management to Enable Energy- and Carbon-Efficient CO 2 Electrolysis (Final Technical Report)

The rapid growth and plummeting cost of solar energy have spurred growing interest in using CO 2 electrolysis to produce chemicals and fuels as an alternative to conventional petrochemical processes. High-temperature (>800 °C) solid oxide electrolyzers that convert CO 2 into CO and O 2 have recently become commercially available. Low-temperature electrolysis cells offer the prospect of more convenient and flexible operation, which is critical for utilizing intermittent solar energy, and provide access to more valuable C 2+ products such as ethylene, ethanol, and propanol. Over the past 10 years, research in this area has yielded substantial progress in both fundamental understanding of the requisite electrocatalytic reactions and design of prototype devices. Leveraging insights from fuel cells and membrane water electrolyzers, researchers have developed electrolysis cells with gas diffusion electrodes (GDE) that have demonstrated high CO 2 electrolysis current densities (>100 mA cm –2 ) as well as promising selectivity and stability. Despite these advances, the energy efficiency (electrical energy-to-product) and carbon efficiency (CO 2 -to-product) of low-temperature CO 2 electrolysis remain far too low for large-scale deployment. A preponderance of evidence indicates that the principal source of efficiency losses is the rapid and thermodynamically favorable reaction of CO 2 with hydroxide (OH – ) to form carbonate (CO 3 2– ). Carbonate formation imposes steady-state electrolysis conditions that result in large voltage and CO 2 losses for all known (photo)electrochemical CO 2 cells. While much current research remains focused on CO 2 reduction catalyst design, this largely overlooked CO 3 2– problem presents a fundamental scientific barrier to creating a viable electrochemical option for converting solar energy into chemicals and fuels. The project pursues an integrated, multi-PI research effort that establishes a fundamental science of CO 3 2– management. PI Kanan and Co-PI Mani’s contribution to the project is to evaluate strategies to mitigate the CO 3 2– problem by changing the properties of the electrolyte and the environment in which CO 2 reduction catalysis takes place. Experimental studies showed that electrolytes composed of a high concentration of both CO 3 2– and HCO 3 – , which serve as moderately alkaline buffers, improved the cell voltage by compared to all-HCO 3 – electrolytes, but these buffered systems still show substantial CO 2 uptake that reduces pH over time. Computational studies developed a homogenized model of a CO 2 reduction catalyst layer that permits a low-cost exploration of the high-dimensional parameter space associated with catalyst layers on gas diffusion electrodes. The model was validated by accurately reproducing experimental data for the related but simpler reaction of CO reduction and then used to probe the effects of catalyst layer architecture on CO 2 reduction. Minimizing the size of catalyst and hydrophobic domains in the catalyst layer is predicted to mitigate CO 3 2– formation and thereby enable prolonged operation at elevated pH. In support of the CO 2 electrolysis studies, a new method for rapidly prototyping electrochemical cells was developed and validated. The method uses a combination of 3D printing and electroless plating to generate conductive cell components for evaluating new cell designs. The carbonate problem encompasses mass transport processes and acid-base reactions that are relevant to many other electrochemical systems. Investigation of strategies to address the carbonate problem led to an additional line of inquiry into the physicochemical phenomena that determine the efficiency of electrochemical acid-base production, which has numerous applications in the broader field of carbon management. New strategies for using the supporting electrolyte to inhibit H + /OH – recombination in electrochemical acid-base production were evaluated, leading to the development of a novel acid-base producing system that eliminates the need for ion exchange membranes and exhibits promising efficiency and current densities for scalable applications.

25 ENERGY STORAGE↗
DOE OSTI2024

Isotopically labelled inorganic carbon delivered to algalcultures via bubbler bottle

This protocol describes a method for delivering labelled inorganic carbon as 13 CO 2 to algal cultures by bubbling air through a solution of H 13 CO 3 - , and then into the culture. We developed this method to deliver label to cultures grown under continuous bubbling with air, without the use of 13 CO 2 labelled gas and the necessary equipment to mix labelled gas with air at near-atmospheric levels. Bubbling precludes the more common approach of adding H 13 CO 3 - label directly to the media, because dissolved HCO 3 - is in equilibrium with atmospheric CO 2 . Thus, excess HCO 3 - added to a solution will leave the solution as CO 2 gas as it equilibrates. Bubbling rapidly accelerates this equilibration which is typically diffusion limited. The method described here takes advantage of this aspect of carbonate chemistry, and uses a solution of H 13 CO 3 - —which is less expensive and more convenient than 13 CO 2 gas—to generate a flux of 13 CO 2 that can be bubbled into a culture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A bicarbonate-rich liquid condensed phase in non-saturated solutions in the absence of divalent cations

Bicarbonate (HCO 3 - ) and sodium (Na + )-containing solutions contain droplets of a separate, bicarbonate-rich liquid condensed phase (LCP) that have higher concentrations of HCO 3 - relative to the bulk solution in which they reside. The existence and composition of the LCP droplets has been investigated by nanoparticle tracking analysis, nuclear magnetic resonance spectroscopy, refractive index measurements and X-ray pair distribution function analysis. The bicarbonate-rich LCP species is a previously unaccounted-for, ionic phenomenon which occurs even in solutions with solely monovalent cations. Its existence requires re-evaluation of models used to describe and model aqueous solution physicochemistry, especially those used to describe and model carbonate mineral formation.

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

LoTSS Jellyfish Galaxies. IV. Enhanced Star Formation on the Leading Half of Cluster Galaxies and Gas Compression in IC3949

With Mapping Nearby Galaxies at APO integral field spectroscopy, we present a resolved analysis of star formation for 29 jellyfish galaxies in nearby clusters, identified from radio continuum imaging taken by the Low Frequency Array. Simulations predict enhanced star formation on the "leading half" (LH) of galaxies undergoing ram pressure stripping, and in this work we report observational evidence for this elevated star formation. The dividing line (through the galaxy center) that maximizes this star formation enhancement is systematically tied to the observed direction of the ram-pressure-stripped tail, suggesting a physical connection between ram pressure and this star formation enhancement. We also present a case study on the distribution of molecular gas in one jellyfish galaxy from our sample, IC3949, using Atacama Large Millimeter/submillimeter Array CO J = 1 – 0, HCN J = 1 – 0, and HCO + J = 1 – 0 observations from the ALMA MaNGA Quenching and Star Formation Survey. The H2 depletion time (as traced by CO) in IC3949 ranges from ~1 Gyr in the outskirts of the molecular gas disk to ~11 Gyr near the galaxy center. IC3949 shows a clear region of enhanced star formation on the LH of the galaxy where the average depletion time is ~2.7 Gyr, in line with the median value for the galaxy on the whole. Dense gas tracers, HCN and HCO + , are only detected at the galaxy center and on the LH of IC3949. Our results favor a scenario in which ram pressure compresses the interstellar medium, promoting the formation of molecular gas that in turn fuels a localized increase of star formation.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1972

A discussion of CO and O on Venus and Mars

The absorption of solar ultraviolet radiation in the wavelength range 2000 to 2200 A by CO2 strongly reduces the dissociation rate of HCl on Venus. The Cl catalytic reaction for the rapid recombination of O and CO and the yellow coloration of the Venus haze by OCl(-) and Cl3(-) appears to be unlikely. At the time of the Martian dust storm, the dissociation of H2O in the vicinity of the surface may vanish. The increase of dissociation at high altitudes, however, can be the source of H atoms in the upper atmosphere. The H atoms from the dissociation of hydrides may catalyze the recombination of CO and O in the lower atmospheres of these planets according to the following scheme: H + CO + M yields HCO + M, and HCO + O yields H + CO2. In the case of Venus, there may be other kinds of sinks for the photodissociation products, and its chemical environment might be more complex than that of Mars.

Shimizu, M.↗
NASA NTRS1971

Photoionization of methanol and formaldehyde

Photoions produced in methanol and formaldehyde by radiation in the spectral region 450-1150 A were analyzed mass spectrometrically, and their relative yields were determined as a function of wavelength. First ionization potentials were determined, and the ion yield curves were interpreted in terms of ionization processes in conjunction with other data. Fragment ions were detected on mass numbers of 31, 30, 29, 15, and 14 for methanol, and 29, 2, and 1 for formaldehyde. The associated appearance potentials were determined and were used to calculate heats of formation of the ions CH2OH(+) and HCO(+), and the radicals CH3, CH2, and HCO.

Warneck, P.↗
NASA NTRS1975

Rotational excitation of molecular ions in interstellar clouds

Rate constants for rotational excitation of N2H(+) by low-energy collisions with He have been obtained from accurate quantum-mechanical calculations. Rates for excitation of HCO(+) and rates for excitation by collisions with H2 are expected to be qualitatively similar. The excitation rate for molecular ions is found to be only slightly faster than that for similar neutral species, and not much faster as had been previously suggested. The implications of this for interpreting microwave observations of interstellar N2H(+) and HCO(+) are discussed.

Green, S.↗
NASA NTRS1978

Nonequilibrium chemistry in shocked molecular clouds

The gas-phase chemistry is studied behind a 10-km/s shock propagating into a dense molecular cloud. The principal conclusions are that: the concentrations of certain molecules (CO, NH3, HCN, N2) are unperturbed by the shock; other molecules (H2CO, CN, HCO(+)) are greatly decreased in abundance; and substantial amounts of H2O, HCO, and CH4 are produced. Approximately 1 million yr (independent of the density) must elapse after shock passage before chemical equilibrium is attained.

Iglesias, E. R.↗
NASA NTRS1981

Some new results on shock chemistry in IC 443

New observations have been made of CO, CO-13, SiO, SO, H2CO, HCO(+), N2H(+), CS, OCS, HCN, and OH in the shocked clouds of IC 443. It is found that at position IC 443 B, (1) the shocked CO is optically thin; (2) the HCO(+)/CO abundance ratio is 4-9 x 10 to the -4 th, representing a tenfold enhancement over that of normal interstellar clouds; (3) there is no enhancement of SO or SIO, as occurs in Orion KL; and (4) there is optically thin preshock OH, confirming a hundredfold enhancement of the OH/CO ratio in the shock.

Denoyer, L. K.↗
NASA NTRS1982

The rotational spectra of HCNH/+/ and COH/+/ from quantum mechanical calculations

A description is provided of ab initio molecular orbital calculations designed to provide accurate predictions for the J = 1 to 0 rotational line of the candidate interstellar molecules HCNH(+) and COH(+). The former is believed to be important in the formation of both HCN and HNC in the interstellar medium. The latter, a metastable isomer of HCO(+), was first proposed as an interstellar molecule by Herbst et al. (1976). Attention is given to thermochemical arguments that this molecule can be formed in the same reactions which are proposed to form HCO(+), taking into account theoretical data which establish its stability to intramolecular rearrangement. Rotational constants are derived by applying an empirical correction to the ab initio rotational constants.

Defrees, D. J.↗
NASA NTRS1984

Metastability of isoformyl ions in collisions with helium and hydrogen

The stability of HOC(+) ions under conditions in interstellar molecular clouds is considered. In particular, the possibility that collisions with helium or hydrogen will induce isomerization to the stable HCO(+) form is examined theoretically. Portions of the electronic potential energy surfaces for interaction with He and H atoms are obtained from standard quantum mechanical calculations. Collisions with He atoms are found to be totally ineffective for inducing isomerization. Collisions with H atoms are found to be ineffective at low interstellar temperatures owing to a small (about 500 K) barrier in the entrance channel; at higher temperatures where this barrier can be overcome, however, collisions with hydrogen atoms do result in conversion to the stable HCO(+) form. Although detailed calculations are not presented, it is argued that low-energy collisions with H2 molecules are also ineffective in destroying the metastable ion.

Green, S.↗
NASA NTRS1984

Energetics of the protonation of CO - Implications for the observation of HOC(+) in dense interstellar clouds

A number of molecular species on the H3CO(+) energy hypersurface is examined. Ab initio molecular orbital theory is used to determine the structures and relative energetics of the two isomers of HCO(+) and HOC(+) together with the affinity of CO for protonation at either end. The proton affinities of H2 and H2CO are also examined. The calculations are performed using large basis sets and include the effects of electron correlation. The calculated vibrational frequencies are used to correct for zero point energy differences. The results show that the proton affinities of H2 and CO to form HOC(+) are within 1 kcal of each other. The calculations demonstrate that there is no thermodynamic driving force to form HOC(+) in collisions of H3(+) with CO, and that the formation of HCO(+) in such collisions is very exoergic. A plausible mechanism is suggested to explain the differences observed between the laboratory and the interstellar medium.

Dixon, D.↗
NASA NTRS1986

Interstellar isomers

Both observational and theoretical studies of molecular clouds are hindered by many difficulties. One way to partially circumvent the difficulties of characterizing the chemistry within these objects is to study the relative abundances of isomers which are synthesized from a common set of precursors. Unfortunately, only one such system has been confirmed, the HCN/HNC pair of isomers. While the basic outlines of its chemistry have been known for some years, there are still many aspects of the chemistry which are unclear. Another potential pair of isomers is HCO+/HOC+; HCO+ is an abundant instellar molecule and a tentative identification of HOC+ has been made in Sgr B2. This identification is being challenged, however, based on theoretical and laboratory evidence that HOC+ reacts with H2. Another potential pair of interstellar isomers is methyl cyanide (CH3CN, acetonitrile) and methyl isocyanide (CH3NC). The cyanide is well known, however the isocyanide has yet to be observed despite theoretical predictions that appreciable quantities should be present.

Defrees, D.↗
NASA NTRS1986

MM and subMM molecular line observations of the southwest lobe of L1551: Evidence of a shell structure

Observations have been made of the southwest outflow lobe of L1551 in several millimeter and submillimeter molecular lines. Maps have been made in the J=3-2 and J=2-1 transitions of CO over areas of 7.5 by 2.5 arc minutes and 5 by 5 arc minutes respectively at UKIRT. More detailed maps have also been made in the J=2-1 CO transition over an area of about 6 by 3.5 arc minutes at the NRAO 12m telescope. Additional observations of the J=4-3 transitions of HCN, HCO(+) abd H(13)CO(+) were made at selected positions. The HC(+) J=4-3 transition was detected at several positions along the outflow axis and at the position of IRS 5. Similarly the HCN J=4-3 transition was detected at the position of IRS 5 and also at a position close to HH29. However, the J=4-3 transition of H(13)CO(+) was bit detected at the position of IRS 5 even through it was observed at the position close to HH29 with a peak corrected antenna temperature of 0.23K at a V(LSR) of 1 km s(-1). The detection of the J=4-3 transitions of both HCO(+) and H(13)CO(+) close to the position of HH29 suggest the presence of very dense gas in this region. LVG analysis of the various molecular lines observed give a kinetic temperature between 10 and 15K and a density from 10(5) to 10(6) cm(-3) at the position of IRS 5 at the ambient cloud velocity. At the position close to HH29 LVG analysis of the CO observations gives a density between 10(3) and 10(4) cm(-3) at a kinetic temperature of 25k for a V(LSR) of 0 km s(-1). To the southwest of HH29 there is a large decrease in both the linewidth and intensity of CO emission. This may be due to the interaction between the outflow and a dense clump of gas which gives rise to HH29. The maps of the CO J=3-2 and CO J=2-1 emission integrated in 3.25 km s intervals show the shell structure postulated by Snell and Schloerb (1985).

Rainey, R.↗