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DOE OSTI2021

Thermodynamic and Kinetic Modeling of Co-utilization of Glucose and Xylose for 2,3-BDO Production by Zymomonas mobilis

Prior engineering of the ethanologen Zymomonas mobilis has enabled it to metabolize xylose and to produce 2,3-butanediol (2,3-BDO) as a dominant fermentation product. When co-fermenting with xylose, glucose is preferentially utilized, even though xylose metabolism generates ATP more efficiently during 2,3-BDO production on a BDO-mol basis. To gain a deeper understanding of Z. mobilis metabolism, we first estimated the kinetic parameters of the glucose facilitator protein of Z. mobilis by fitting a kinetic uptake model, which shows that the maximum transport capacity of glucose is seven times higher than that of xylose, and glucose is six times more affinitive to the transporter than xylose. With these estimated kinetic parameters, we further compared the thermodynamic driving force and enzyme protein cost of glucose and xylose metabolism. It is found that, although 20% more ATP can be yielded stoichiometrically during xylose utilization, glucose metabolism is thermodynamically more favorable with 6% greater cumulative Gibbs free energy change, more economical with 37% less enzyme cost required at the initial stage and sustains the advantage of the thermodynamic driving force and protein cost through the fermentation process until glucose is exhausted. Glucose-6-phosphate dehydrogenase (g6pdh), glyceraldehyde-3-phosphate dehydrogenase (gapdh) and phosphoglycerate mutase (pgm) are identified as thermodynamic bottlenecks in glucose utilization pathway, as well as two more enzymes of xylose isomerase and ribulose-5-phosphate epimerase in xylose metabolism. Acetolactate synthase is found as potential engineering target for optimized protein cost supporting unit metabolic flux. Pathway analysis was then extended to the core stoichiometric matrix of Z. mobilis metabolism. Growth was simulated by dynamic flux balance analysis and the model was validated showing good agreement with experimental data. Dynamic FBA simulations suggest that a high agitation is preferable to increase 2,3-BDO productivity while a moderate agitation will benefit the 2,3-BDO titer. Taken together, this work provides thermodynamic and kinetic insights of Z. mobilis metabolism on dual substrates, and guidance of bioengineering efforts to increase hydrocarbon fuel production.

23-butanediol↗

DOE OSTI2024

Theoretical analysis of the OH-initiated atmospheric oxidation reactions of imidazole

Imidazoles are present in Earth's atmosphere in both the gas-phase and in aerosol particles, and have been implicated in the formation of brown carbon aerosols. The gas-phase oxidation of imidazole (C 3 N 2 H 4 ) by hydroxyl radicals has been shown to be preferentially initiated via OH-addition to position C5, producing the 5-hydroxyimidazolyl radical adduct. However, the fate of this adduct upon reaction with O 2 in the atmospheric gas-phase is currently unknown. We employed an automated approach to investigate the reaction mechanism and kinetics of imidazole's OH-initiated gas-phase oxidation, in the presence of O 2 and NO x . The explored mechanism included reactions available to first-generation RO 2 radicals, as well as alkoxyl radicals produced from RO 2 + NO reactions. Product distributions were obtained by assembling and solving a master equation, under conditions relevant to the Earth's atmosphere. Our calculations show a complex, branched reaction mechanism, which nevertheless converges to yield two major closed-shell products: 4H-imidazol-4-ol (4H-4ol) and N,N′-diformylformamidine (FMF). At 298 K and 1 atm, we estimate the yields of 4H-4ol and FMF from imidazole oxidation initiated via OH-addition to position C5 to be 34 : 66, 12 : 85 and 2 : 95 under 10 ppt, 100 ppt and 1 ppb of NO respectively. This work also revealed O 2 -migration pathways between the α-N-imino peroxyl radical isomers. This reaction channel is fast for the first-generation RO 2 radicals, and may be important during the atmospheric oxidation of other unsaturated organic nitrogen compounds as well.

Almeida, Thomas Golin↗

DOE OSTI2020

Mesoporous silica-encapsulated gold core–shell nanoparticles for active solvent-free benzyl alcohol oxidation

Silica-encapsulated gold core@shell nanoparticles (Au@SiO2 CSNPs) were synthesized via a bottom-up procedure and used to catalyze the selective oxidation of benzyl alcohol. The pore size, morphology, crystallinity and composition of Au@SiO2 was evaluated using non-local density functional theory, transmission electron microscopy, high-energy x-ray diffraction and inductively coupled plasma-mass spectroscopy, respectively. The nanoparticles exhibit a mesoporous shell with an average thickness of 25.5 Å which can enhance selectivity via preferential transport of the desired product (i.e., benzaldehyde) relative to larger, undesired products (i.e, benzoic acid/benzyl benzoate). GC-FID analysis revealed the addition of potassium carbonate to the solvent-free oxidation of benzyl alcohol increased conversion from 17.3 to 60.4% while decreasing selectivity from 98.7 to 75.0%. Under equivalent conditions, a bare gold nanoparticle control catalyst deposited on a silica support with a similar gold surface area took 6 times as long to reach the same conversion, achieving only 49.4% selectivity. These results suggest that the pore size distribution within the inert silica shell of Au@SiO2 CSNPs inhibits the formation of undesired products to facilitate the selective oxidation of benzaldehyde despite a basic environment, which reduces selectivity under typical conditions. The CSNPs demonstrated a much lower activation energy than the Au-SiO2 control catalyst, 37 ± 1.9 kJ/mol and 72 ± 7.1 kJ/mol, respectively. Thiele modulus analysis indicates the CSNP pore structure does not create a mass transport limitation due to the nano-scale path of diffusion through the pore structure to the active surface. The lower activation energy and mesopore distribution together suggest the Au@SiO2 catalyst demonstrates higher activity through beneficial in-pore orientation, both reducing competitive adsorption and promoting a single, lower activation energy mechanistic pathway.

benzyl alcohol oxidation, catalysis, confinement↗

DOE OSTI2019

Molecular-Level Design of Heterogeneous Chiral Catalysts

A recent major focus of catalyst research has been on improving the selectivity or atom efficiency of catalytic processes. Perhaps the most subtle and difficult form of selectivity to control is enantioselectivity, a catalyst’s ability to preferentially yield one enantiomer of a chiral product. Since two enantiomers are identical in all respects except for their mirror reflection symmetry, both are formed in non-chiral environments at exactly equal rates; only by introducing some type of chiral modification to the system can the rate of formation of one enantiomer be favored over the other. This has been successfully achieved for homogeneous-phase, organometallic catalysts, but the empirical development of heterogeneous-phase analogs has proven elusive. The design of such heterogeneous-phase catalysts would obviate the need for inefficient purification steps to remove the heavy-metal catalysts. The goal of the proposed research by the Chiral Catalysis Group is to understand the interactions of prochiral reactants on chirally modified surfaces that lead to the preferential formation of one enantiomer over the other. There are two general concepts for designing heterogeneous-phase enantioselective catalysts. The first adopts the strategy used in homogeneous phase, by adding a chiral modifier to the surface. This approach, while conceptually simple has challenges associated with modifying an extended surface. The second concept, which is unique to extended surfaces, is the idea of creating surfaces that are themselves naturally chiral. A fundamental understanding of the interactions that control enantioselectivity will enable the Chiral Catalysis Group to develop the concepts necessary to design novel, heterogenous catalytic materials. Enantioselectivity is also central to catalytic processes that underpin the pharmaceutical and agrochemical industries. With funding from the Department of Energy, the Chiral Catalysis Group has played a leading role in developing a fundamental understanding of chiral catalysis and of the adsorbate structures, interactions and kinetic effects that control heterogenous-phase enantioselectivity. The proposed research program is organized conceptually around three types of enantiospecific interactions: interactions with naturally chiral surfaces; those with modified surfaces categorized as chirally templated surfaces; and one-to-one interactions of prochiral molecules with chiral surface modifiers. Our specific goals are to: (1) determine the structures of chiral surfaces, prochiral reactants, chiral products and chiral modifiers; (2) understand the enantiospecific interactions that occur between prochiral reactants and chiral products with chirally modified surfaces; (3) develop methods for detection of enantiospecific surface phenomena; and (4) elucidate enantioselective reaction pathways and the interactions that control them. The range of expertise within the Chiral Catalysis Group includes molecular-scale theory, surface science experiments, state-of-the-art spectroscopic, kinetic and atomic-scale imaging capabilities carried out in vacuum and under more-realistic liquid- and gas-phase environments complemented by catalytic measurements. By fully integrating such a breadth of approaches and extensive expertise, the Chiral Catalysis Group will, for the first time, be able to understand, rationally design and then control active sites for optimal enantioselectivity. In addition to having a significant impact on the field of chiral catalysis, the proposed research program will further our general understanding of the molecular-scale origins of catalytic selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Enabling residential heating decarbonization through hydronic low-temperature thermal distribution using forced-air assistive devices

Space heating represents approximately one-tenth of the United States’ energy use and has a breadth of potential for emission reduction. An element of space heating, hydronic heat distribution methods, use water supply temperatures up to 82.2 °C (180 °F). However, this operating temperature can be incompatible with high-efficiency heat generation systems, which typically provide heating temperatures of up to 60 °C (140 °F). In this work, a low-cost retrofit solution is developed using experimentally validated computational tools by incorporating an airflow distributor that preferentially directs the airflow from a fan to enhance heat transfer over the finned-tube heat exchanger found in conventional baseboards. The same heat output of traditional baseboard heat distribution systems operating at higher water supply temperatures (71.1 – 82.2 °C) can also be achieved at lower temperatures (≤60 °C). Specifically, results indicate that the technology can produce more than a 46.7% improvement in the heat transfer output at temperatures as low as 60 °C (140 °F), effectively matching the same output range achieved by 71.1 – 82.2 °C (160–180 °F) water supply temperatures. An important benefit of this solution is that it utilizes the existing infrastructure as opposed to requiring the replacement of the entire distribution system. Additionally, this technology enables existing building infrastructure to be coupled with newer, high-efficiency heating systems such as condensing boilers, solar-thermal systems, and geothermal/air-to-water heat pumps that may produce lower water supply temperatures (60 °C). A geospatially resolved techno-economic and environmental analysis is completed and presented to further understand the equivalent carbon footprint of enabling higher efficiency heat generation systems with the improved efficiency heat distribution system disclosed. Using 2021 grid-average emission factors, an emission reduction of up to a 67.5% decrease (2658 kgCO 2 /yr) for a single-family home, depending on state and climate region, could be realized by replacing a traditional natural gas-fired boiler with an air-to-water heat pump coupled to the same high-temperature heat distribution system along with the low-cost retrofit solution. A complete CO 2 emission reduction of 6688 kgCO 2 /yr, depending on state and climate region, could be realized if all electricity is further renewably sourced. Thus, this study provides a possible pathway towards enabling the reduction of operational emissions in space heating.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

NASA NTRS2010

Discovery of Carbonate-Rich Outcrops in the Gusev Crater Columbia Hills by the MER Rover Spirit

The chemical composition, global abundance, distribution, and formation pathways of carbonates are central to understanding aqueous processes, climate, and habitability of early Mars. The Mars Exploration Rover (MER) Spirit analyzed a series of olivine-rich outcrops while descending from the summit region of Husband Hill into the Inner Basin of the Columbia Hills of Gusev Crater to the eastern edge of the El Dorado ripple field in late 2005. Reanalysis of Spirit s mineralogical data from the Moessbauer Spectrometer (MB) and the Miniature Thermal Emission Spectrometer (Mini-TES) and chemical data from the Alpha Particle X-Ray Spectrometer (APXS) in 2010, coupled with new laboratory data for carbonate-bearing samples, lead to identification of carbonate in one of the outcrops (Comanche) [Morris, R.V., et al., Science, 329, 421-424]. The carbonate is rich in magnesium and iron (Mc62Sd25Cc11Rh2, assuming all Ca and Mn is associated with the carbonate) and is a major component of the Comanche outcrops (16 to 34 wt.%). The mineralogical, chemical, and abundance data are constrained in multiple, mutually consistent ways by the MER analyses. For example, a low-Ca carbonate is required by the MB and APXS data and is consistent with Mini-TES data. Three spectral features attributable to fundamental infrared vibrational modes of low-Ca carbonate are present in the Mini-TES spectra of Comanche outcrops. The average composition of Comanche carbonate approximates the average composition of the carbonate globules in Martian meteorite ALH 84001. Analogy with ALH 84001, terrestrial, and synthetic carbonate globules suggests that Comanche carbonate precipitated from aqueous solutions under hydrothermal conditions at near neutral pH in association with volcanic activity during the Noachian era. Comanche outcrop morphology suggests they are remnants of a larger carbonate-bearing formation that evolved in ultramafic rock and then preferentially eroded by a combination of aeolian abrasion and chemical decomposition by exposure to acid-sulfate vapors/solutions. The high carbonate concentration in the Comanche outcrops supports climate models involving a CO2 greenhouse gas on a wet and warm early Mars and subsequent sequestering of at least part of that atmosphere in carbonate minerals.

Morris, Richard V.↗

NASA NTRS1996

Neurofilament protein is differentially distributed in subpopulations of corticocortical projection neurons in the macaque monkey visual pathways

Previous studies of the primate cerebral cortex have shown that neurofilament protein is present in pyramidal neuron subpopulations displaying specific regional and laminar distribution patterns. In order to characterize further the neurochemical phenotype of the neurons furnishing feedforward and feedback pathways in the visual cortex of the macaque monkey, we performed an analysis of the distribution of neurofilament protein in corticocortical projection neurons in areas V1, V2, V3, V3A, V4, and MT. Injections of the retrogradely transported dyes Fast Blue and Diamidino Yellow were placed within areas V4 and MT, or in areas V1 and V2, in 14 adult rhesus monkeys, and the brains of these animals were processed for immunohistochemistry with an antibody to nonphosphorylated epitopes of the medium and heavy molecular weight subunits of the neurofilament protein. Overall, there was a higher proportion of neurons projecting from areas V1, V2, V3, and V3A to area MT that were neurofilament protein-immunoreactive (57-100%), than to area V4 (25-36%). In contrast, feedback projections from areas MT, V4, and V3 exhibited a more consistent proportion of neurofilament protein-containing neurons (70-80%), regardless of their target areas (V1 or V2). In addition, the vast majority of feedback neurons projecting to areas V1 and V2 were located in layers V and VI in areas V4 and MT, while they were observed in both supragranular and infragranular layers in area V3. The laminar distribution of feedforward projecting neurons was heterogeneous. In area V1, Meynert and layer IVB cells were found to project to area MT, while neurons projecting to area V4 were particularly dense in layer III within the foveal representation. In area V2, almost all neurons projecting to areas MT or V4 were located in layer III, whereas they were found in both layers II-III and V-VI in areas V3 and V3A. These results suggest that neurofilament protein identifies particular subpopulations of corticocortically projecting neurons with distinct regional and laminar distribution in the monkey visual system. It is possible that the preferential distribution of neurofilament protein within feedforward connections to area MT and all feedback projections is related to other distinctive properties of these corticocortical projection neurons.

Non-NASA Center↗

NASA NTRS2004

Did the Pre-RNA World Rest Upon DNA Molecules?

The isolation of a DNA sequence that catalyzes the ligation of oligodeoxynucleotides via the formation of 3' - 5' phosphodiester linkage significance in selection experiments has been reported. Ball recently used this to discuss the possibility that natural DNA molecules may have formed in the primitive Earth leading to the origin of life. As noted by Ferris and Usher, if metabolic pathways evolved backwards, it could be argued that the biosynthesis of 2-deoxyribose from ribose suggests that RNA came from DNA. As summarized elsewhere, there are several properties of deoxyribose which could be interpreted to support the possibility that DNA-like molecules arose prior to the RNA world. For example, 2-deoxyribose is slightly more soluble than ribose (which may have been an advantage in a drying pool scenario), may have been more reactive under possible prebiotic conditions (it forms a nucleoside approx. 150 times faster than ribose with the alternative base urazole at 25 C), while it decomposes in solution (approximately 2.6 times more slowly than ribose at 100 C). Other advantages of DNA over RNA are that it has one fewer chiral center, has a greater stability at the 8.2 pH value of the current oceans, and does not has the 2'5' and 3'5' ambiguity in polymerizations. Yet, there is strong molecular biological and biochemical evidence that RNA was featured in the biology well before the last common ancestor. The presence of sugar acids, including both ribo- and deoxysugar acids, in the 4.6 Ga old Murchison meteorite suggest that both may have been available in the primitive Earth, derived from the accretion of extraterrestrial sources and/or from endogenous processes involving formaldehyde and its derivatives. However, the abiotic synthesis of deoxyribose, ribose, and other sugars from glyceraldehyde and acetaldehyde under alkaline conditions is inefficient and unespecific. Although sugars are labile compounds, the role of cyanamide or borate minerals in the stabilization of the cyclic forms of ribose and other pentoses has recently been demonstrated. Nonetheless, the assumption either RNA or DNA was the first genetic material needs to be supplemented by laboratory models demonstrating that the prebiotic synthesis of activated beta-D-(deoxy)ribonucleotides and their polymers was feasible. As of today such evidence is lacking, and there is no convincing synthesis of any nucleotide, since all model experiments produce complex mixtures of products in which there is no preferential synthesis of chiral D-nucleotides. This strongly suggests that both DNA and RNA may have been preceded by pairing structures much simpler than extant nucleic acids. It is doubtful that DNA molecules, or indeed other (de0xy)ribofuranoid oligonucleotides formed the basis of these as yet undescribed pre-RNA worlds.

Lazcano, Antonio↗